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Zinc in PDB 3mbj: Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form)

Protein crystallography data

The structure of Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form), PDB code: 3mbj 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) 29.59 / 2.10
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 161.627, 161.627, 76.138, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 21

Other elements in 3mbj:

The structure of Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form) (pdb code 3mbj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form), PDB code: 3mbj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3mbj

Go back to Zinc Binding Sites List in 3mbj
Zinc binding site 1 out of 3 in the Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn291

b:24.8
occ:0.50
OD2 A:ASP279 2.0 21.7 1.0
ND1 A:HIS276 2.1 16.4 1.0
CE1 A:HIS276 2.9 12.5 1.0
CG A:ASP279 2.9 23.5 1.0
OD1 A:ASP279 3.1 22.8 1.0
CG A:HIS276 3.2 16.6 1.0
CB A:HIS276 3.6 14.3 1.0
NE2 A:HIS276 4.1 15.5 1.0
CD2 A:HIS276 4.3 12.2 1.0
CB A:ASP279 4.3 26.1 1.0
CA A:HIS276 4.4 15.1 1.0
O A:HOH422 4.7 51.0 1.0
O A:HIS276 4.9 14.9 1.0

Zinc binding site 2 out of 3 in 3mbj

Go back to Zinc Binding Sites List in 3mbj
Zinc binding site 2 out of 3 in the Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn292

b:36.2
occ:1.00
OD2 A:ASP96 2.2 20.4 1.0
CG A:ASP96 2.8 17.5 1.0
OD1 A:ASP96 2.9 14.4 1.0
CG A:GLN92 4.2 18.1 1.0
CB A:ASP96 4.2 17.8 1.0
NE2 A:GLN92 4.4 17.8 1.0
CD A:GLN92 4.6 20.9 1.0
O A:GLN92 4.9 16.6 1.0

Zinc binding site 3 out of 3 in 3mbj

Go back to Zinc Binding Sites List in 3mbj
Zinc binding site 3 out of 3 in the Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Putative Phosphomethylpyrimidine Kinase (BT_4458) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.10 A Resolution (Rhombohedral Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn293

b:39.5
occ:1.00
O A:HOH398 2.0 36.2 1.0
O A:HOH354 2.1 23.8 1.0
O A:HOH317 2.3 17.2 1.0
O A:HOH332 2.4 23.3 1.0
O A:HOH337 2.4 24.5 1.0
O A:HOH411 3.8 36.8 1.0
O A:HOH346 4.0 23.5 1.0
OD1 A:ASP111 4.1 22.6 1.0
OE2 A:GLU148 4.1 20.4 1.0
OE1 A:GLU148 4.1 16.6 1.0
O A:HOH349 4.1 24.7 1.0
OD2 A:ASP111 4.2 22.5 1.0
CG2 A:VAL113 4.2 21.3 1.0
O4 A:SO4295 4.3 55.5 1.0
O A:HOH372 4.3 27.1 1.0
OH A:TYR121 4.4 25.2 1.0
ND2 A:ASN145 4.4 20.7 1.0
CG A:ASP111 4.5 22.8 1.0
CD A:GLU148 4.5 19.1 1.0
CG1 A:VAL113 4.6 21.9 1.0
CA A:GLY223 4.8 18.4 1.0
CB A:VAL113 4.8 22.0 1.0
CA A:VAL113 5.0 21.8 1.0
CG A:ASN145 5.0 19.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Dec 16 04:34:45 2020

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