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Xenon in PDB 1kqn: Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad

Enzymatic activity of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad

All present enzymatic activity of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad:
2.7.7.1;

Protein crystallography data

The structure of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad, PDB code: 1kqn was solved by T.Zhou, O.Kurnasov, D.R.Tomchick, D.D.Binns, N.V.Grishin, V.E.Marquez, A.L.Osterman, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 130.816, 90.879, 136.585, 90.00, 116.85, 90.00
R / Rfree (%) 21.8 / 25

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Xenon atom in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad (pdb code 1kqn). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 15 binding sites of Xenon where determined in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad, PDB code: 1kqn:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 15 in 1kqn

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Xenon binding site 1 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe748

b:88.2
occ:1.00
O A:LEU88 3.5 33.8 1.0
C A:LEU88 3.7 33.3 1.0
O A:HOH804 3.7 26.7 1.0
CA A:LEU88 3.9 31.2 1.0
O A:SER87 3.9 27.3 1.0
O A:GLN89 4.3 31.3 1.0
C A:GLN89 4.3 32.6 1.0
N A:GLN89 4.3 34.5 1.0
CG A:LYS90 4.4 35.6 1.0
N A:LYS90 4.5 31.9 1.0
CA A:LYS90 4.6 33.9 1.0
C A:SER87 4.8 27.4 1.0
N A:LEU88 4.8 28.5 1.0
CA A:GLN89 4.9 34.0 1.0
CD2 A:LEU88 4.9 26.6 1.0

Xenon binding site 2 out of 15 in 1kqn

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Xenon binding site 2 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe749

b:94.3
occ:1.00
CD1 A:LEU27 3.4 37.1 1.0
OE1 A:GLU215 3.5 40.7 1.0
O A:MET23 3.6 26.3 1.0
OD1 A:ASN219 3.7 50.3 1.0
CD A:GLU215 3.8 41.6 1.0
CG A:MET23 3.9 37.5 1.0
N A:LEU27 3.9 27.3 1.0
N1A A:NAD777 4.0 41.8 1.0
CB A:ARG26 4.0 27.2 1.0
C2A A:NAD777 4.1 41.2 1.0
CD1 A:LEU30 4.1 32.2 1.0
CA A:LEU27 4.1 27.9 1.0
OE2 A:GLU215 4.2 45.1 1.0
CG A:ASN219 4.3 54.0 1.0
SD A:MET23 4.3 51.3 1.0
CB A:ASN219 4.4 52.1 1.0
CG A:GLU215 4.4 35.4 1.0
C A:ARG26 4.4 27.7 1.0
CG1 A:VAL186 4.5 20.0 1.0
C A:MET23 4.5 25.6 1.0
CB A:LEU27 4.5 32.9 1.0
CG A:LEU27 4.6 37.7 1.0
O A:HOH790 4.6 31.2 1.0
CA A:MET23 4.7 26.8 1.0
C6A A:NAD777 4.7 41.0 1.0
CA A:ARG26 4.8 27.6 1.0
CB A:MET23 4.8 32.4 1.0
N3A A:NAD777 4.9 42.0 1.0

Xenon binding site 3 out of 15 in 1kqn

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Xenon binding site 3 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe750

b:0.2
occ:1.00
CZ A:PHE196 3.9 26.2 1.0
OG A:SER200 3.9 26.9 1.0
CE2 A:PHE196 4.1 27.7 1.0
CB A:SER200 4.1 26.8 1.0
CB A:PHE163 4.2 28.6 1.0
O A:HOH783 4.3 26.1 1.0
O A:PHE163 4.3 29.1 1.0
C A:PHE163 4.5 30.1 1.0
CD1 A:LEU203 4.5 22.3 1.0
N A:ALA164 4.6 31.3 1.0
CA A:ALA164 4.7 33.1 1.0
CB A:ALA164 4.7 32.2 1.0
CG A:LEU203 4.8 25.8 1.0
CE1 A:PHE196 4.9 28.9 1.0
CD1 A:ILE174 4.9 27.5 1.0

Xenon binding site 4 out of 15 in 1kqn

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Xenon binding site 4 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe751

b:0.0
occ:1.00
O B:HOH858 3.4 38.2 1.0
O B:HOH873 3.4 44.9 1.0
OE1 B:GLU71 4.3 29.6 1.0
CB B:GLU71 4.4 24.9 1.0
O B:HOH849 4.4 38.4 1.0
O B:HOH844 4.5 31.8 1.0
CG B:GLU71 4.7 27.7 1.0
CD B:GLU71 4.7 29.9 1.0
O B:GLU71 4.8 27.0 1.0

Xenon binding site 5 out of 15 in 1kqn

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Xenon binding site 5 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe752

b:1.0
occ:1.00
CB B:SER200 3.9 34.2 1.0
OG B:SER200 4.0 34.6 1.0
CB B:PHE163 4.3 34.8 1.0
CZ B:PHE196 4.3 37.5 1.0
O B:PHE163 4.4 39.6 1.0
CE2 B:PHE196 4.4 37.1 1.0
O B:HOH808 4.4 39.7 1.0
C B:PHE163 4.6 38.5 1.0
CD1 B:LEU203 4.6 34.4 1.0
N B:ALA164 4.8 40.1 1.0
CA B:ALA164 4.9 40.8 1.0

Xenon binding site 6 out of 15 in 1kqn

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Xenon binding site 6 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe755

b:0.9
occ:1.00
OE1 B:GLU215 3.5 42.9 1.0
CD B:GLU215 3.5 43.0 1.0
O B:MET23 3.6 24.2 1.0
OE2 B:GLU215 3.8 48.4 1.0
CG B:MET23 3.9 38.0 1.0
CD1 B:LEU27 3.9 34.2 1.0
N B:LEU27 4.0 25.4 1.0
CG B:GLU215 4.2 37.0 1.0
CB B:ARG26 4.2 26.0 1.0
CD1 B:LEU30 4.2 30.4 1.0
CA B:LEU27 4.2 25.8 1.0
O B:HOH870 4.2 38.1 1.0
N1A B:NAD778 4.2 50.5 1.0
CG B:ARG26 4.3 32.3 1.0
O B:HOH871 4.4 50.9 1.0
C B:ARG26 4.4 24.7 1.0
C B:MET23 4.4 27.1 1.0
CG1 B:VAL186 4.5 23.6 1.0
CG B:LEU27 4.5 33.6 1.0
CB B:LEU27 4.6 28.8 1.0
CA B:MET23 4.6 28.7 1.0
C2A B:NAD778 4.6 49.2 1.0
SD B:MET23 4.6 50.1 1.0
O B:HOH782 4.7 24.8 1.0
C6A B:NAD778 4.7 51.1 1.0
CB B:MET23 4.8 32.1 1.0
O B:ARG26 4.9 27.9 1.0
CA B:ARG26 4.9 25.7 1.0
N6A B:NAD778 4.9 52.9 1.0

Xenon binding site 7 out of 15 in 1kqn

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Xenon binding site 7 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe760

b:96.6
occ:1.00
CD2 B:LEU27 3.5 33.5 1.0
O B:HIS24 3.7 22.5 1.0
CB B:LEU27 3.8 28.8 1.0
CB B:ALA13 3.8 23.4 1.0
C4B B:NAD778 4.1 44.0 1.0
CD1 B:LEU154 4.1 27.6 1.0
CA B:HIS24 4.1 23.6 1.0
CG B:LEU27 4.1 33.6 1.0
O4B B:NAD778 4.1 43.3 1.0
CE1 B:PHE28 4.1 28.2 1.0
CB B:HIS24 4.2 25.0 1.0
ND1 B:HIS24 4.2 30.7 1.0
C B:HIS24 4.3 22.6 1.0
CD1 B:LEU27 4.3 34.2 1.0
CD1 B:PHE28 4.4 28.7 1.0
CE2 B:PHE17 4.5 19.8 1.0
C5B B:NAD778 4.6 42.4 1.0
CG B:HIS24 4.7 27.3 1.0
CZ B:PHE17 4.7 22.7 1.0
C1B B:NAD778 4.9 45.4 1.0
O B:HOH810 5.0 38.1 1.0

Xenon binding site 8 out of 15 in 1kqn

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Xenon binding site 8 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe753

b:0.4
occ:1.00
O C:HOH806 3.3 35.0 1.0
OE1 C:GLU215 3.5 48.6 1.0
CD C:GLU215 3.5 47.4 1.0
OE2 C:GLU215 3.5 46.5 1.0
CD1 C:LEU27 3.6 34.7 1.0
O C:MET23 3.6 20.6 1.0
CD1 C:LEU30 3.8 28.8 1.0
CB C:ARG26 3.9 24.2 1.0
CG C:MET23 3.9 37.0 1.0
N1A C:NAD779 4.1 43.6 1.0
N C:LEU27 4.1 24.9 1.0
O C:HOH895 4.2 43.3 1.0
C2A C:NAD779 4.3 43.3 1.0
CG C:GLU215 4.3 40.6 1.0
CA C:LEU27 4.4 26.8 1.0
CG1 C:VAL186 4.4 24.3 1.0
C C:ARG26 4.5 25.1 1.0
C C:MET23 4.5 23.4 1.0
SD C:MET23 4.6 53.3 1.0
CA C:MET23 4.7 23.6 1.0
O C:HOH815 4.7 29.8 1.0
CB C:LEU27 4.8 28.1 1.0
C6A C:NAD779 4.8 45.1 1.0
CA C:ARG26 4.8 25.0 1.0
CG C:LEU27 4.8 33.8 1.0
CB C:MET23 4.8 29.7 1.0
O C:ASN219 5.0 48.9 1.0
O C:ARG26 5.0 26.2 1.0

Xenon binding site 9 out of 15 in 1kqn

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Xenon binding site 9 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe754

b:0.8
occ:1.00
OG C:SER200 3.8 25.5 1.0
CB C:SER200 3.9 24.9 1.0
CZ C:PHE196 4.0 25.7 1.0
O C:HOH796 4.3 20.7 1.0
CE2 C:PHE196 4.4 26.8 1.0
O C:PHE163 4.4 25.8 1.0
CB C:PHE163 4.4 23.7 1.0
C C:PHE163 4.6 24.8 1.0
CB C:ALA164 4.7 28.2 1.0
CA C:ALA164 4.7 29.2 1.0
N C:ALA164 4.7 25.9 1.0
CD1 C:LEU203 4.8 23.2 1.0
CE1 C:PHE196 4.9 26.4 1.0
CG C:LEU203 5.0 24.5 1.0

Xenon binding site 10 out of 15 in 1kqn

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Xenon binding site 10 out of 15 in the Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Crystal Structure of Nmn/Namn Adenylyltransferase Complexed with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe759

b:51.3
occ:1.00
O C:HOH905 3.5 38.5 1.0
O C:HOH800 3.6 20.3 1.0
O C:LEU88 3.8 33.2 1.0
O C:GLN89 3.9 33.2 1.0
O C:HOH853 3.9 36.7 1.0
O C:SER87 4.0 26.2 1.0
C C:LEU88 4.0 32.1 1.0
C C:GLN89 4.2 33.8 1.0
CG C:LYS90 4.3 35.1 1.0
CA C:LEU88 4.3 28.8 1.0
CA C:LYS90 4.3 34.9 1.0
N C:LYS90 4.4 33.3 1.0
N C:GLN89 4.6 31.7 1.0
CB C:LYS90 4.9 34.1 1.0
C C:SER87 4.9 27.5 1.0

Reference:

T.Zhou, O.Kurnasov, D.R.Tomchick, D.D.Binns, N.V.Grishin, V.E.Marquez, A.L.Osterman, H.Zhang. Structure of Human Nicotinamide/Nicotonic Acid Mononucleotide Adenylyltransferase. Basis For the Dual Substrate Specificity and Activation of the Oncolytic Agent Tiazofurin. J.Biol.Chem. V. 277 13148 2003.
ISSN: ISSN 0021-9258
PubMed: 11788603
DOI: 10.1074/JBC.M111469200
Page generated: Wed Dec 16 02:39:23 2020

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