Atomistry » Nickel » PDB 1jhj-1q0d » 1qwz
Atomistry »
  Nickel »
    PDB 1jhj-1q0d »
      1qwz »

Nickel in PDB 1qwz: Crystal Structure of Sortase B From S. Aureus Complexed with Mtset

Protein crystallography data

The structure of Crystal Structure of Sortase B From S. Aureus Complexed with Mtset, PDB code: 1qwz was solved by Y.Zong, S.K.Mazmanian, O.Schneewind, S.V.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.71 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.482, 61.566, 45.727, 90.00, 91.58, 90.00
R / Rfree (%) 18.3 / 22.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset (pdb code 1qwz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset, PDB code: 1qwz:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1qwz

Go back to Nickel Binding Sites List in 1qwz
Nickel binding site 1 out of 4 in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset


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 Sortase B From S. Aureus Complexed with Mtset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni246

b:45.5
occ:0.50
ND1 A:HIS17 3.5 14.4 1.0
O A:HOH485 3.9 40.6 1.0
ND1 A:HIS16 3.9 23.7 1.0
N A:HIS17 4.1 16.3 1.0
CE1 A:HIS17 4.2 15.8 1.0
CA A:HIS16 4.3 18.3 1.0
CB A:HIS16 4.5 20.0 1.0
CG A:HIS17 4.7 13.4 1.0
CG A:HIS16 4.7 20.8 1.0
C A:HIS16 4.8 17.2 1.0
CE1 A:HIS16 5.0 21.7 1.0
CB A:HIS17 5.0 14.1 1.0

Nickel binding site 2 out of 4 in 1qwz

Go back to Nickel Binding Sites List in 1qwz
Nickel binding site 2 out of 4 in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset


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 Sortase B From S. Aureus Complexed with Mtset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni247

b:17.5
occ:1.00
NE2 A:HIS19 2.0 9.7 1.0
NE2 A:HIS17 2.1 13.5 1.0
CD2 A:HIS19 2.9 11.6 1.0
CE1 A:HIS19 3.1 12.3 1.0
CD2 A:HIS17 3.1 12.8 1.0
CE1 A:HIS17 3.1 15.8 1.0
CG A:HIS19 4.1 10.3 1.0
ND1 A:HIS19 4.1 9.0 1.0
ND1 A:HIS17 4.2 14.4 1.0
CG A:HIS17 4.2 13.4 1.0
O A:HOH426 4.5 25.4 1.0

Nickel binding site 3 out of 4 in 1qwz

Go back to Nickel Binding Sites List in 1qwz
Nickel binding site 3 out of 4 in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Sortase B From S. Aureus Complexed with Mtset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni248

b:20.4
occ:1.00
NE2 A:HIS104 2.2 21.1 1.0
CE1 A:HIS104 2.9 22.8 1.0
CD2 A:HIS104 3.4 22.9 1.0
ND1 A:HIS104 4.1 22.1 1.0
CG A:HIS104 4.4 20.5 1.0
CD2 A:LEU98 4.9 15.7 1.0

Nickel binding site 4 out of 4 in 1qwz

Go back to Nickel Binding Sites List in 1qwz
Nickel binding site 4 out of 4 in the Crystal Structure of Sortase B From S. Aureus Complexed with Mtset


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Sortase B From S. Aureus Complexed with Mtset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni249

b:23.4
occ:1.00
O A:HOH387 3.1 30.4 1.0
N A:HIS19 3.5 13.3 1.0
CD2 A:HIS19 3.8 11.6 1.0
O A:HOH397 3.9 42.1 1.0
CB A:HIS19 4.0 12.5 1.0
O A:HIS17 4.1 15.6 1.0
CA A:HIS18 4.2 14.2 1.0
CG A:HIS19 4.2 10.3 1.0
CA A:HIS19 4.3 12.8 1.0
C A:HIS18 4.3 12.9 1.0
CA A:ILE25 4.6 27.4 1.0
N A:SER26 4.6 34.3 1.0
O A:HIS19 4.7 13.1 1.0
CD A:LYS33 4.7 24.6 1.0
O A:SER26 4.7 39.3 1.0
CG2 A:ILE25 4.8 26.9 1.0
NH2 A:ARG36 4.9 31.7 1.0
O A:HIS24 5.0 23.2 1.0
CG1 A:ILE25 5.0 26.2 1.0

Reference:

Y.Zong, S.K.Mazmanian, O.Schneewind, S.V.Narayana. The Structure of Sortase B, A Cysteine Transpeptidase That Tethers Surface Protein to the Staphylococcus Aureus Cell Wall Structure V. 12 105 2004.
ISSN: ISSN 0969-2126
PubMed: 14725770
DOI: 10.1016/J.STR.2003.11.021
Page generated: Fri Sep 25 08:00:19 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy