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Nickel in PDB 3htn: Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution, PDB code: 3htn was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 1.50
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 90.688, 90.688, 53.888, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 16.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution (pdb code 3htn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution, PDB code: 3htn:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3htn

Go back to Nickel Binding Sites List in 3htn
Nickel binding site 1 out of 2 in the Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:23.4
occ:0.40
O A:HOH410 1.7 25.8 0.7
O A:HOH410 1.8 21.6 0.3
NE2 A:HIS131 2.2 17.9 1.0
ND1 A:HIS147 2.2 17.8 0.5
NE2 A:HIS133 2.3 15.1 1.0
O C:HOH619 2.7 21.4 1.0
CE1 A:HIS147 3.0 19.1 0.5
CD2 A:HIS131 3.1 17.2 1.0
CD2 A:HIS133 3.2 14.9 1.0
CE1 A:HIS131 3.2 20.5 1.0
CE1 A:HIS133 3.2 15.7 1.0
CG A:HIS147 3.3 14.8 0.5
CG A:HIS147 3.5 13.7 0.5
ND1 A:HIS147 3.6 15.0 0.5
CB A:HIS147 3.7 14.2 0.5
CB A:HIS147 3.8 14.9 0.5
O A:HOH309 3.8 34.6 1.0
CD2 A:HIS147 3.9 12.7 0.5
CE1 A:HIS147 4.1 13.1 0.5
O A:HOH260 4.2 24.2 1.0
OE1 C:GLU113 4.2 20.2 1.0
NE2 A:HIS147 4.2 14.8 0.5
NE2 A:HIS147 4.2 16.4 0.5
CG A:HIS131 4.3 16.0 1.0
ND1 A:HIS131 4.3 17.1 1.0
ND1 A:HIS133 4.4 16.4 1.0
CG A:HIS133 4.4 15.2 1.0
CD2 A:HIS147 4.4 14.1 0.5
CA A:HIS147 4.6 14.1 0.5
CA A:HIS147 4.6 13.8 0.5
CD C:GLU113 4.7 20.4 1.0
O C:HOH598 4.8 27.2 1.0
O C:HOH611 4.8 20.5 1.0
O A:HOH288 4.8 26.8 1.0
OE2 C:GLU113 4.9 21.0 1.0

Nickel binding site 2 out of 2 in 3htn

Go back to Nickel Binding Sites List in 3htn
Nickel binding site 2 out of 2 in the Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Putative Dna Binding Protein (BT_1116) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni208

b:34.4
occ:0.40
NE2 B:HIS61 2.2 23.0 1.0
O B:HOH500 2.9 33.3 1.0
CD2 B:HIS61 3.0 20.7 1.0
CE1 B:HIS61 3.3 25.6 1.0
ND2 B:ASN60 4.1 18.3 1.0
CG B:HIS61 4.2 16.7 1.0
ND1 B:HIS61 4.3 23.1 1.0
OD2 C:ASP175 4.4 30.1 0.3
CD2 C:LEU176 4.8 20.2 1.0
CG B:ASN60 4.9 15.3 1.0
O C:HOH696 5.0 36.1 1.0
CB B:ASN60 5.0 14.3 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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