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Chlorine 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:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Human Glutamine-Dependent Nad+ Synthetase Complexed with Naad+, Amp, Pyrophosphate, and MG2+, PDB code: 6ofb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6ofb

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Chlorine binding site 1 out of 9 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 Chlorine with other atoms in the Cl 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:Cl905

b:74.5
occ:1.00
 N A:ARG145 3.7 76.4 1.0
CA A:PRO144 3.9 64.7 1.0
CB A:PRO144 4.3 67.8 1.0
C A:PRO144 4.3 74.3 1.0
O A:HOH1014 4.5 61.5 1.0
CB A:ARG145 4.5 91.3 1.0
CA A:ARG145 4.7 81.9 1.0

Chlorine binding site 2 out of 9 in 6ofb

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Chlorine binding site 2 out of 9 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 Chlorine with other atoms in the Cl 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
A:Cl906

b:63.8
occ:1.00
 NE A:ARG300 3.7 70.0 1.0
N A:ARG300 3.8 55.7 1.0
NH2 A:ARG300 3.9 58.5 1.0
CA A:PRO299 4.1 50.2 1.0
CZ A:ARG300 4.3 59.0 1.0
CB A:ARG300 4.5 53.2 1.0
C A:PRO299 4.5 57.1 1.0
O A:TYR298 4.7 67.3 1.0
CG A:ARG300 4.7 52.0 1.0
CA A:ARG300 4.7 55.8 1.0
CD A:ARG300 4.8 59.5 1.0
O A:ARG300 4.9 52.3 1.0
CB A:PRO299 5.0 45.5 1.0

Chlorine binding site 3 out of 9 in 6ofb

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Chlorine binding site 3 out of 9 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl907

b:64.2
occ:1.00
 NH2 A:ARG476 3.5 61.0 1.0
NE A:ARG476 3.7 68.9 1.0
N B:GLY508 3.7 71.2 1.0
ND1 B:HIS507 3.9 88.0 1.0
CZ A:ARG476 4.1 63.9 1.0
CB B:HIS507 4.4 73.2 1.0
CA B:GLY508 4.4 66.1 1.0
CA B:HIS507 4.6 74.6 1.0
CG B:HIS507 4.6 80.2 1.0
C B:HIS507 4.6 76.9 1.0
CD A:ARG476 4.9 67.0 1.0
CE1 B:HIS507 5.0 90.3 1.0

Chlorine binding site 4 out of 9 in 6ofb

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Chlorine binding site 4 out of 9 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl908

b:84.9
occ:1.00
 NH2 A:ARG548 3.0 97.5 1.0
CL A:CL909 3.1 0.1 1.0
NE A:ARG548 3.2 97.8 1.0
CE A:LYS544 3.3 88.1 1.0
CG2 A:VAL360 3.5 77.6 1.0
NZ A:LYS544 3.5 96.4 1.0
CZ A:ARG548 3.5 98.8 1.0
CB A:ALA571 3.6 0.6 1.0
CB A:VAL360 4.2 79.3 1.0
CD A:ARG548 4.4 87.9 1.0
MG A:MG904 4.5 0.6 1.0
CD A:LYS544 4.7 79.6 1.0
CG A:ARG548 4.8 71.8 1.0
CA A:ALA571 4.8 0.5 1.0
NH1 A:ARG548 4.9 94.6 1.0

Chlorine binding site 5 out of 9 in 6ofb

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Chlorine binding site 5 out of 9 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl909

b:0.1
occ:1.00
 MG A:MG904 2.9 0.6 1.0
O2 A:POP903 2.9 0.7 1.0
CL A:CL908 3.1 84.9 1.0
CB A:ALA571 3.5 0.6 1.0
CG2 A:VAL360 3.5 77.6 1.0
N A:VAL360 3.5 75.4 1.0
CA A:ALA571 3.8 0.5 1.0
O3 A:POP903 3.9 0.4 1.0
P1 A:POP903 3.9 0.5 1.0
NZ A:LYS544 4.0 96.4 1.0
CB A:VAL360 4.0 79.3 1.0
CA A:GLY359 4.2 82.6 1.0
C A:GLY359 4.4 76.9 1.0
CA A:VAL360 4.4 74.4 1.0
O1 A:POP903 4.7 0.5 1.0
N A:ALA571 4.7 0.5 1.0
CE A:LYS544 4.8 88.1 1.0
C A:ALA571 4.9 0.9 1.0

Chlorine binding site 6 out of 9 in 6ofb

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Chlorine binding site 6 out of 9 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl905

b:71.4
occ:1.00
 NH2 B:ARG476 3.0 74.4 1.0
NE B:ARG476 3.6 70.5 1.0
CZ B:ARG476 3.8 70.1 1.0
N A:GLY508 3.9 65.0 1.0
CA A:GLY508 4.5 68.7 1.0
CB A:HIS507 4.6 67.4 1.0
CA A:HIS507 4.7 73.8 1.0
C A:HIS507 4.8 68.7 1.0
CD B:ARG476 4.9 74.4 1.0
CG A:HIS507 4.9 75.7 1.0

Chlorine binding site 7 out of 9 in 6ofb

Go back to Chlorine Binding Sites List in 6ofb
Chlorine binding site 7 out of 9 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl906

b:58.2
occ:1.00
 N B:SER475 3.5 83.1 1.0
CB B:SER475 3.7 73.7 1.0
CA B:SER475 4.3 77.0 1.0
CB B:SER474 4.4 81.7 1.0
CA B:SER474 4.5 84.6 1.0
C B:SER474 4.5 83.2 1.0
OG B:SER475 4.8 86.0 1.0

Chlorine binding site 8 out of 9 in 6ofb

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Chlorine binding site 8 out of 9 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl907

b:98.7
occ:1.00
 NH1 B:ARG548 2.7 62.2 0.5
CL B:CL908 2.9 0.6 1.0
NH2 B:ARG548 2.9 73.2 0.5
NE B:ARG548 3.3 73.3 0.5
CB B:ALA571 3.4 0.5 1.0
CZ B:ARG548 3.5 74.2 0.5
CE B:LYS544 3.7 78.3 1.0
CG2 B:VAL360 3.7 64.1 1.0
CZ B:ARG548 4.0 65.9 0.5
NZ B:LYS544 4.3 79.2 1.0
CD B:ARG548 4.4 70.9 0.5
CD B:ARG548 4.5 69.8 0.5
CB B:VAL360 4.5 64.7 1.0
CA B:ALA571 4.6 0.1 1.0
NE B:ARG548 4.7 68.3 0.5
NH1 B:ARG548 4.8 72.3 0.5
CG B:ARG548 4.8 0.5 0.5
CG B:ARG548 4.9 0.4 0.5
NH2 B:ARG548 4.9 65.1 0.5
N B:ALA571 5.0 0.9 1.0

Chlorine binding site 9 out of 9 in 6ofb

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Chlorine binding site 9 out of 9 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl908

b:0.6
occ:1.00
 CL B:CL907 2.9 98.7 1.0
MG B:MG904 3.0 0.4 1.0
CG2 B:VAL360 3.3 64.1 1.0
CB B:ALA571 3.3 0.5 1.0
O1 B:POP903 3.4 0.7 1.0
N B:VAL360 3.7 68.6 1.0
CB B:VAL360 3.8 64.7 1.0
CA B:ALA571 3.8 0.1 1.0
NZ B:LYS544 4.1 79.2 1.0
O3 B:POP903 4.2 0.4 1.0
P1 B:POP903 4.3 0.5 1.0
CA B:VAL360 4.4 66.6 1.0
CA B:GLY359 4.5 74.2 1.0
CE B:LYS544 4.5 78.3 1.0
C B:GLY359 4.6 67.2 1.0
N B:ALA571 4.6 0.9 1.0
NH1 B:ARG548 4.8 62.2 0.5
C B:ALA571 5.0 0.4 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 Jul 29 12:39:39 2024

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