Magnesium in PDB 6ofb: Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+

Enzymatic activity of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+

All present enzymatic activity of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+:
6.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+, PDB code: 6ofb was solved by W.Chuenchor, T.I.Doukov, B.Gerratana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.40 / 2.84
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.250, 198.890, 219.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.7

Other elements in 6ofb:

The structure of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+ also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+ (pdb code 6ofb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+, PDB code: 6ofb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ofb

Go back to Magnesium Binding Sites List in 6ofb
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:0.6
occ:1.00
 N A:VAL360 2.7 75.4 1.0
O5 A:POP903 2.7 0.9 1.0
N A:ASP361 2.8 79.9 1.0
CL A:CL909 2.9 0.1 1.0
O2 A:POP903 2.9 0.7 1.0
O3 A:POP903 3.0 0.4 1.0
NZ A:LYS544 3.0 96.4 1.0
CA A:VAL360 3.2 74.4 1.0
CB A:VAL360 3.2 79.3 1.0
P1 A:POP903 3.4 0.5 1.0
C A:VAL360 3.4 75.6 1.0
OD1 A:ASP361 3.5 90.6 1.0
C A:GLY359 3.5 76.9 1.0
CG A:ASP361 3.6 90.2 1.0
P2 A:POP903 3.7 0.2 1.0
CG2 A:VAL360 3.8 77.6 1.0
CA A:ASP361 3.9 76.0 1.0
CB A:ASP361 3.9 82.1 1.0
O6 A:POP903 3.9 0.7 1.0
O A:POP903 4.0 0.5 1.0
OD2 A:ASP361 4.0 94.5 1.0
CA A:GLY359 4.0 82.6 1.0
CE A:LYS544 4.2 88.1 1.0
O A:GLY359 4.4 78.2 1.0
CG1 A:VAL360 4.4 76.4 1.0
CL A:CL908 4.5 84.9 1.0
O A:VAL360 4.6 74.3 1.0
O1 A:POP903 4.8 0.5 1.0
N A:SER362 5.0 70.0 1.0

Magnesium binding site 2 out of 2 in 6ofb

Go back to Magnesium Binding Sites List in 6ofb
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:0.4
occ:1.00
 O5 B:POP903 2.7 0.5 1.0
N B:ASP361 2.8 66.4 1.0
O1 B:POP903 2.9 0.7 1.0
N B:VAL360 2.9 68.6 1.0
O3 B:POP903 3.0 0.4 1.0
CL B:CL908 3.0 0.6 1.0
CB B:VAL360 3.2 64.7 1.0
NZ B:LYS544 3.2 79.2 1.0
OD1 B:ASP361 3.3 94.1 1.0
CA B:VAL360 3.3 66.6 1.0
P1 B:POP903 3.4 0.5 1.0
CG B:ASP361 3.5 95.8 1.0
C B:VAL360 3.5 65.3 1.0
C B:GLY359 3.6 67.2 1.0
P2 B:POP903 3.7 89.2 1.0
CB B:ASP361 3.9 78.5 1.0
CA B:ASP361 3.9 66.2 1.0
O4 B:POP903 3.9 82.4 1.0
O B:POP903 4.0 0.5 1.0
CG2 B:VAL360 4.0 64.1 1.0
OD2 B:ASP361 4.0 0.8 1.0
CA B:GLY359 4.0 74.2 1.0
CE B:LYS544 4.2 78.3 1.0
O B:GLY359 4.3 65.3 1.0
CG1 B:VAL360 4.4 73.2 1.0
O B:VAL360 4.7 62.8 1.0
O2 B:POP903 4.8 0.3 1.0
N B:SER362 4.9 65.2 1.0
C B:ASP361 5.0 62.1 1.0

Reference:

W.Chuenchor, T.I.Doukov, K.Chang, M.Resto, C.S.Yun, B.Gerratana. Different Ways to Transport Ammonia in Human and Mycobacterium Tuberculosis Nad+ Synthetases Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-019-13845-4
Page generated: Mon Dec 14 23:43:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy