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Zinc in PDB 6dz8: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)

Protein crystallography data

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C), PDB code: 6dz8 was solved by J.A.N.Alexander, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.16 / 1.86
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.511, 89.730, 77.489, 90.00, 98.09, 90.00
R / Rfree (%) 17.5 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) (pdb code 6dz8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C), PDB code: 6dz8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dz8

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Zinc binding site 1 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:65.1
occ:1.00
OE2 A:GLU357 1.7 49.9 1.0
HE2 A:HIS362 1.7 34.0 1.0
NE2 A:HIS362 2.4 28.3 1.0
CD A:GLU357 2.7 46.6 1.0
CE1 A:HIS362 3.2 26.4 1.0
HE1 A:HIS362 3.2 31.6 1.0
O A:HOH619 3.3 52.5 1.0
OE1 A:GLU357 3.3 51.2 1.0
CD2 A:HIS362 3.4 21.6 1.0
HD2 A:HIS362 3.7 25.9 1.0
CG A:GLU357 3.9 39.1 1.0
HG2 A:GLU357 3.9 46.9 1.0
HG11 A:VAL355 4.1 49.3 1.0
HG12 A:VAL355 4.1 49.3 1.0
HG3 A:GLU357 4.2 46.9 1.0
ND1 A:HIS362 4.3 27.1 1.0
CG A:HIS362 4.4 21.0 1.0
HG2 A:PRO376 4.5 31.8 1.0
CG1 A:VAL355 4.5 41.1 1.0
O A:HOH501 4.8 31.0 1.0
HB A:VAL355 4.9 32.8 1.0
HD1 A:HIS362 5.0 32.6 1.0

Zinc binding site 2 out of 4 in 6dz8

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Zinc binding site 2 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:52.1
occ:0.36
OE1 A:GLU380 2.0 73.4 1.0
HG2 A:GLU336 2.8 59.4 1.0
CD A:GLU380 3.0 63.9 1.0
HB2 A:GLU380 3.1 46.1 1.0
HB3 A:GLU380 3.2 46.1 1.0
CB A:GLU380 3.5 38.5 1.0
CG A:GLU336 3.5 49.5 1.0
CD A:GLU336 3.6 58.9 1.0
HB2 A:GLU336 3.7 51.6 1.0
CG A:GLU380 3.8 48.7 1.0
OE1 A:GLU336 3.8 60.3 1.0
OE2 A:GLU380 3.9 62.9 1.0
HD2 A:HIS382 3.9 73.7 1.0
CB A:GLU336 4.1 43.0 1.0
OE2 A:GLU336 4.2 65.4 1.0
HG3 A:GLU380 4.3 58.4 1.0
HB3 A:GLU336 4.3 51.6 1.0
HG3 A:GLU336 4.3 59.4 1.0
HG2 A:GLU380 4.5 58.4 1.0
CD2 A:HIS382 4.8 61.4 1.0
CA A:GLU380 4.9 28.8 1.0

Zinc binding site 3 out of 4 in 6dz8

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Zinc binding site 3 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:36.1
occ:0.57
OE2 B:GLU336 1.9 80.1 1.0
NE2 B:HIS382 2.0 65.0 1.0
CD2 B:HIS382 2.7 58.8 1.0
HD2 B:HIS382 2.7 70.5 1.0
HD1 B:TYR334 3.0 52.8 1.0
CD B:GLU336 3.2 80.0 1.0
CE1 B:HIS382 3.2 65.7 1.0
CD1 B:TYR334 3.4 44.1 1.0
HE1 B:HIS382 3.5 78.9 1.0
HB3 B:TYR334 3.7 78.9 1.0
O B:HOH580 3.8 46.8 1.0
HG2 B:GLU336 3.8 77.7 1.0
CE1 B:TYR334 3.9 73.1 1.0
HE1 B:TYR334 3.9 87.8 1.0
CG B:HIS382 3.9 55.7 1.0
OE1 B:GLU336 4.0 87.3 1.0
CG B:TYR334 4.0 71.0 1.0
CG B:GLU336 4.1 64.7 1.0
ND1 B:HIS382 4.1 62.4 1.0
CB B:TYR334 4.4 65.7 1.0
HG3 B:GLU336 4.5 77.7 1.0
HA B:GLU336 4.7 55.0 1.0
HB2 B:TYR334 4.8 78.9 1.0
CZ B:TYR334 4.9 65.9 1.0
HD1 B:HIS382 4.9 74.9 1.0
CD2 B:TYR334 5.0 66.3 1.0

Zinc binding site 4 out of 4 in 6dz8

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Zinc binding site 4 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:35.1
occ:0.50
OE2 B:GLU357 1.7 48.9 1.0
NE2 B:HIS362 2.3 35.0 1.0
CD B:GLU357 2.8 36.0 1.0
CE1 B:HIS362 3.0 23.9 1.0
HE1 B:HIS362 3.0 28.6 1.0
OE1 B:GLU357 3.3 51.5 1.0
CD2 B:HIS362 3.3 33.7 1.0
O B:HOH651 3.4 48.7 1.0
HD2 B:HIS362 3.6 40.5 1.0
HG2 B:GLU357 3.9 38.4 1.0
HG11 B:VAL355 3.9 37.9 1.0
CG B:GLU357 3.9 32.0 1.0
HG12 B:VAL355 4.0 37.9 1.0
ND1 B:HIS362 4.1 33.4 1.0
HG3 B:GLU357 4.3 38.4 1.0
CG B:HIS362 4.3 28.8 1.0
CG1 B:VAL355 4.4 31.5 1.0
HB B:VAL355 4.6 39.8 1.0
HG2 B:PRO376 4.7 34.4 1.0
O B:HOH524 4.8 38.8 1.0
HD1 B:HIS362 4.9 40.0 1.0

Reference:

R.Maya-Martinez, J.A.N.Alexander, C.F.Otten, I.Ayala, D.Vollmer, J.Gray, C.M.Bougault, A.Burt, C.Laguri, M.Fonvielle, M.Arthur, N.C.J.Strynadka, W.Vollmer, J.P.Simorre. Recognition of Peptidoglycan Fragments By the Transpeptidase PBP4 Fromstaphylococcus Aureus. Front Microbiol V. 9 3223 2018.
ISSN: ESSN 1664-302X
PubMed: 30713527
DOI: 10.3389/FMICB.2018.03223
Page generated: Wed Dec 16 11:41:39 2020

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