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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: Tue Oct 1 13:22:41 2024

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