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Zinc in PDB 5ls3: Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation, PDB code: 5ls3 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 1.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.886, 59.886, 276.115, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation (pdb code 5ls3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation, PDB code: 5ls3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5ls3

Go back to Zinc Binding Sites List in 5ls3
Zinc binding site 1 out of 5 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation


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 Metallo-Beta-Lactamase Spm-1 with Y58C Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:21.1
occ:1.00
O B:HOH566 1.9 20.0 1.0
NE2 B:HIS197 2.0 21.2 1.0
ND1 B:HIS110 2.1 22.0 1.0
NE2 B:HIS108 2.1 19.0 1.0
CD2 B:HIS108 3.0 20.0 1.0
CD2 B:HIS197 3.0 20.6 1.0
CE1 B:HIS197 3.0 23.5 1.0
CE1 B:HIS110 3.0 21.3 1.0
CG B:HIS110 3.0 21.1 1.0
CE1 B:HIS108 3.1 20.2 1.0
ZN B:ZN402 3.3 28.9 1.0
CB B:HIS110 3.4 20.1 1.0
OD1 B:ASP112 3.8 24.4 1.0
O B:HOH656 3.9 66.5 1.0
SG B:CYS216 4.1 24.2 1.0
CB B:CYS216 4.1 24.7 1.0
ND1 B:HIS197 4.1 21.9 1.0
O B:HOH638 4.1 24.1 1.0
CG B:HIS197 4.1 21.1 1.0
NE2 B:HIS110 4.1 23.1 1.0
CG B:HIS108 4.2 18.1 1.0
CD2 B:HIS110 4.2 23.5 1.0
ND1 B:HIS108 4.2 20.4 1.0
OD2 B:ASP112 4.3 25.7 1.0
CG B:ASP112 4.4 25.2 1.0
CA B:HIS110 4.8 19.7 1.0
O B:HOH663 4.9 59.6 1.0

Zinc binding site 2 out of 5 in 5ls3

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Zinc binding site 2 out of 5 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation


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 Metallo-Beta-Lactamase Spm-1 with Y58C Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:28.9
occ:1.00
O B:HOH566 2.1 20.0 1.0
NE2 B:HIS258 2.1 23.9 1.0
OD2 B:ASP112 2.1 25.7 1.0
SG B:CYS216 2.3 24.2 1.0
O B:HOH638 2.7 24.1 1.0
CD2 B:HIS258 3.0 24.2 1.0
CE1 B:HIS258 3.1 25.3 1.0
CG B:ASP112 3.1 25.2 1.0
O B:HOH656 3.2 66.5 1.0
CB B:CYS216 3.3 24.7 1.0
ZN B:ZN401 3.3 21.1 1.0
OD1 B:ASP112 3.4 24.4 1.0
O B:HOH512 3.7 41.8 1.0
NE2 B:HIS197 4.1 21.2 1.0
CG B:HIS258 4.2 24.4 1.0
ND1 B:HIS258 4.2 24.8 1.0
NE2 B:HIS108 4.3 19.0 1.0
CE1 B:HIS108 4.3 20.2 1.0
CE1 B:HIS197 4.5 23.5 1.0
CB B:ASP112 4.5 22.0 1.0
O B:HOH643 4.5 40.6 1.0
CA B:CYS216 4.5 22.1 1.0
CD2 B:HIS197 4.9 20.6 1.0

Zinc binding site 3 out of 5 in 5ls3

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Zinc binding site 3 out of 5 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation


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 Metallo-Beta-Lactamase Spm-1 with Y58C Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:30.9
occ:1.00
OD2 B:ASP35 2.0 36.0 1.0
OD2 A:ASP35 2.0 37.8 1.0
NE2 B:HIS33 2.1 34.5 1.0
NE2 A:HIS33 2.1 35.2 1.0
CG A:ASP35 2.7 33.7 1.0
OD1 A:ASP35 2.7 35.8 1.0
CG B:ASP35 2.7 34.0 1.0
OD1 B:ASP35 2.8 35.4 1.0
CE1 A:HIS33 3.0 40.6 1.0
CE1 B:HIS33 3.0 38.9 1.0
CD2 B:HIS33 3.0 31.6 1.0
CD2 A:HIS33 3.2 33.3 1.0
O B:HOH624 3.9 74.8 1.0
ND1 B:HIS33 4.1 34.3 1.0
CB A:ASP35 4.2 32.6 1.0
ND1 A:HIS33 4.2 36.9 1.0
CB B:ASP35 4.2 34.3 1.0
CG B:HIS33 4.2 30.6 1.0
CG A:HIS33 4.3 34.6 1.0
O B:HOH648 4.3 64.4 1.0
O B:HOH503 4.9 66.5 1.0
N B:ASP35 4.9 33.5 1.0
O B:HOH536 5.0 40.0 1.0
O A:HOH674 5.0 52.5 1.0
CA B:ASP35 5.0 32.3 1.0

Zinc binding site 4 out of 5 in 5ls3

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Zinc binding site 4 out of 5 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation


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 Metallo-Beta-Lactamase Spm-1 with Y58C Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:25.6
occ:0.76
OD2 A:ASP112 2.0 28.2 1.0
O A:HOH586 2.0 24.0 1.0
NE2 A:HIS258 2.1 20.5 1.0
SG A:CYS216 2.3 23.4 1.0
CD2 A:HIS258 3.0 20.2 1.0
CG A:ASP112 3.0 24.0 1.0
CE1 A:HIS258 3.1 20.0 1.0
O A:HOH635 3.3 31.8 1.0
OD1 A:ASP112 3.3 23.2 1.0
CB A:CYS216 3.4 25.8 1.0
ZN A:ZN402 3.4 20.3 1.0
O A:HOH660 3.5 46.8 1.0
CG A:HIS258 4.1 19.9 1.0
CE1 A:HIS108 4.1 18.4 1.0
ND1 A:HIS258 4.2 19.9 1.0
NE2 A:HIS108 4.2 19.3 1.0
NE2 A:HIS197 4.2 19.7 1.0
CB A:ASP112 4.4 22.6 1.0
CA A:CYS216 4.5 23.3 1.0
CE1 A:HIS197 4.7 20.8 1.0
O A:HOH578 4.8 24.4 1.0
O A:HOH637 4.9 23.6 1.0
O A:GLY257 4.9 21.6 1.0
O A:ASP112 4.9 21.8 1.0
CA A:GLY257 5.0 19.3 1.0
C A:GLY257 5.0 21.0 1.0
CD2 A:HIS197 5.0 18.4 1.0

Zinc binding site 5 out of 5 in 5ls3

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Zinc binding site 5 out of 5 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 with Y58C Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:20.3
occ:1.00
O A:HOH586 1.9 24.0 1.0
NE2 A:HIS108 2.0 19.3 1.0
ND1 A:HIS110 2.1 21.1 1.0
NE2 A:HIS197 2.1 19.7 1.0
CD2 A:HIS108 3.0 19.2 1.0
CD2 A:HIS197 3.0 18.4 1.0
CG A:HIS110 3.0 20.8 1.0
CE1 A:HIS110 3.0 22.9 1.0
CE1 A:HIS108 3.1 18.4 1.0
CE1 A:HIS197 3.1 20.8 1.0
CB A:HIS110 3.4 20.5 1.0
ZN A:ZN401 3.4 25.6 0.8
O A:HOH660 3.7 46.8 1.0
OD1 A:ASP112 3.8 23.2 1.0
SG A:CYS216 4.0 23.4 1.0
CB A:CYS216 4.1 25.8 1.0
NE2 A:HIS110 4.1 23.6 1.0
CG A:HIS108 4.2 18.1 1.0
CD2 A:HIS110 4.2 21.8 1.0
ND1 A:HIS108 4.2 18.2 1.0
CG A:HIS197 4.2 17.8 1.0
ND1 A:HIS197 4.2 18.5 1.0
OD2 A:ASP112 4.3 28.2 1.0
O A:HOH635 4.4 31.8 1.0
CG A:ASP112 4.4 24.0 1.0
CA A:HIS110 4.8 21.8 1.0

Reference:

M.I.Abboud, P.Hinchliffe, J.Brem, R.Macsics, I.Pfeffer, A.Makena, K.D.Umland, A.M.Rydzik, G.B.Li, J.Spencer, T.D.Claridge, C.J.Schofield. (19) F-uc(Nmr) Reveals the Role of Mobile Loops in Product and Inhibitor Binding By the Sao Paulo Metallo-Beta-Lactamase. Angew. Chem. Int. Ed. Engl. V. 56 3862 2017.
ISSN: ESSN 1521-3773
PubMed: 28252254
DOI: 10.1002/ANIE.201612185
Page generated: Wed Dec 16 06:30:37 2020

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