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Zinc in PDB 4oko: Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa)

Protein crystallography data

The structure of Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa), PDB code: 4oko was solved by G.K.Feld, B.W.Segelke, M.H.Corzett, M.S.Hunter, M.Frank, A.Rasley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.54 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.712, 63.308, 81.689, 70.36, 84.34, 82.53
R / Rfree (%) 21.3 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa) (pdb code 4oko). 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 Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa), PDB code: 4oko:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4oko

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Zinc binding site 1 out of 4 in the Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa)


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 Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:50.1
occ:1.00
OE2 A:GLU89 1.9 31.7 1.0
ND1 A:HIS86 2.0 26.8 1.0
ND1 A:HIS171 2.1 27.9 1.0
OE1 A:GLU89 2.5 33.7 1.0
CD A:GLU89 2.5 35.1 1.0
O A:HOH501 2.5 28.4 1.0
HB3 A:HIS171 2.8 30.1 1.0
CE1 A:HIS86 2.9 30.0 1.0
HB2 A:HIS86 3.0 32.7 1.0
HE1 A:HIS86 3.0 36.0 1.0
CE1 A:HIS171 3.0 30.6 1.0
CG A:HIS86 3.1 26.2 1.0
CG A:HIS171 3.1 28.4 1.0
HE1 A:HIS171 3.2 36.7 1.0
CB A:HIS171 3.4 25.1 1.0
CB A:HIS86 3.5 27.2 1.0
O A:HOH549 3.6 31.1 1.0
HH12 A:ARG129 3.6 52.3 1.0
HB3 A:HIS86 3.9 32.7 1.0
CG A:GLU89 4.0 37.8 1.0
H A:GLU172 4.0 37.3 1.0
NE2 A:HIS86 4.0 29.0 1.0
NH1 A:ARG129 4.1 43.6 1.0
HB2 A:HIS171 4.1 30.1 1.0
CD2 A:HIS86 4.1 27.8 1.0
NE2 A:HIS171 4.2 28.3 1.0
HA A:HIS171 4.2 30.5 1.0
CD2 A:HIS171 4.2 28.5 1.0
HG3 A:GLU89 4.2 45.3 1.0
HH11 A:ARG129 4.3 52.3 1.0
O A:HOH510 4.3 29.9 1.0
O A:GLU172 4.3 37.7 1.0
HG2 A:GLU89 4.4 45.3 1.0
CA A:HIS171 4.4 25.4 1.0
H3 A:ACT402 4.5 56.8 1.0
H A:HIS86 4.5 39.5 1.0
OH A:TYR88 4.5 42.7 1.0
HD22 A:ASN138 4.6 43.8 1.0
N A:GLU172 4.6 31.1 1.0
OXT A:ACT402 4.6 41.4 1.0
OE2 A:GLU272 4.8 32.8 1.0
C A:ACT402 4.8 46.1 1.0
H1 A:ACT402 4.8 56.8 1.0
HE1 A:TYR88 4.8 48.0 1.0
HB2 A:GLU89 4.8 50.2 1.0
CA A:HIS86 4.8 28.3 1.0
HH A:TYR88 4.9 51.3 1.0
HH22 A:ARG129 4.9 55.1 1.0
CH3 A:ACT402 4.9 47.4 1.0
OE1 A:GLU272 4.9 27.9 1.0
N A:HIS86 5.0 32.9 1.0
CB A:GLU89 5.0 41.8 1.0

Zinc binding site 2 out of 4 in 4oko

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Zinc binding site 2 out of 4 in the Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa)


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 Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:61.3
occ:1.00
OE2 B:GLU89 2.0 31.3 1.0
ND1 B:HIS171 2.0 29.7 1.0
ND1 B:HIS86 2.2 34.0 1.0
OE1 B:GLU89 2.6 37.9 1.0
O B:HOH517 2.6 34.6 1.0
CD B:GLU89 2.6 32.6 1.0
HB3 B:HIS171 2.9 31.8 1.0
CE1 B:HIS171 3.0 35.6 1.0
HB2 B:HIS86 3.0 36.5 1.0
CG B:HIS171 3.1 28.1 1.0
HE1 B:HIS171 3.1 42.7 1.0
CE1 B:HIS86 3.1 31.9 1.0
CG B:HIS86 3.2 31.4 1.0
HE1 B:HIS86 3.2 38.3 1.0
CB B:HIS171 3.5 26.5 1.0
O B:HOH514 3.5 33.7 1.0
CB B:HIS86 3.6 30.5 1.0
HB3 B:HIS86 3.9 36.5 1.0
HH22 B:ARG129 4.0 65.7 1.0
HH21 B:ARG129 4.0 65.7 1.0
O B:HOH502 4.1 32.2 1.0
CG B:GLU89 4.1 34.6 1.0
NH2 B:ARG129 4.1 54.8 1.0
NE2 B:HIS171 4.1 30.8 1.0
HB2 B:HIS171 4.1 31.8 1.0
H B:GLU172 4.1 41.4 1.0
H3 B:ACT402 4.1 55.1 1.0
CD2 B:HIS171 4.2 29.1 1.0
NE2 B:HIS86 4.2 35.5 1.0
HA B:HIS171 4.2 34.3 1.0
CD2 B:HIS86 4.3 35.2 1.0
HG3 B:GLU89 4.3 41.6 1.0
O B:GLU172 4.3 36.5 1.0
H1 B:ACT402 4.4 55.1 1.0
CA B:HIS171 4.5 28.6 1.0
H B:HIS86 4.5 40.7 1.0
HG2 B:GLU89 4.5 41.6 1.0
OXT B:ACT402 4.5 46.2 1.0
OE2 B:GLU272 4.5 42.5 1.0
HD22 B:ASN138 4.6 45.2 1.0
OH B:TYR88 4.6 57.9 1.0
CH3 B:ACT402 4.6 46.0 1.0
C B:ACT402 4.6 45.9 1.0
N B:GLU172 4.7 34.5 1.0
CZ B:ARG129 4.8 53.0 1.0
HE1 B:TYR88 4.8 51.8 1.0
OE1 B:GLU272 4.8 34.1 1.0
CA B:HIS86 4.9 31.1 1.0
HB2 B:GLU89 4.9 42.9 1.0
HH B:TYR88 4.9 69.5 1.0
N B:HIS86 4.9 33.9 1.0

Zinc binding site 3 out of 4 in 4oko

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Zinc binding site 3 out of 4 in the Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa)


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 Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:47.6
occ:1.00
ND1 C:HIS171 2.1 31.0 1.0
OE2 C:GLU89 2.1 32.8 1.0
ND1 C:HIS86 2.2 26.3 1.0
O C:HOH501 2.4 25.9 1.0
OE1 C:GLU89 2.5 36.1 1.0
CD C:GLU89 2.6 33.4 1.0
HB3 C:HIS171 2.8 37.9 1.0
HB2 C:HIS86 2.9 31.9 1.0
CE1 C:HIS171 3.0 35.0 1.0
CG C:HIS171 3.1 32.2 1.0
CE1 C:HIS86 3.1 26.1 1.0
HE1 C:HIS171 3.1 42.0 1.0
CG C:HIS86 3.2 25.5 1.0
HE1 C:HIS86 3.2 31.4 1.0
CB C:HIS171 3.4 31.6 1.0
O C:HOH521 3.5 31.9 1.0
CB C:HIS86 3.5 26.6 1.0
HB3 C:HIS86 3.9 31.9 1.0
HH22 C:ARG129 4.0 62.7 1.0
O C:HOH513 4.0 35.1 1.0
H C:GLU172 4.1 37.2 1.0
CG C:GLU89 4.1 35.5 1.0
HH21 C:ARG129 4.1 62.7 1.0
HB2 C:HIS171 4.1 37.9 1.0
NH2 C:ARG129 4.1 52.2 1.0
NE2 C:HIS171 4.1 31.3 1.0
CD2 C:HIS171 4.2 32.4 1.0
HA C:HIS171 4.2 39.4 1.0
NE2 C:HIS86 4.2 28.6 1.0
O C:GLU172 4.3 31.4 1.0
CD2 C:HIS86 4.3 28.2 1.0
HG3 C:GLU89 4.3 42.5 1.0
H2 C:ACT402 4.4 57.8 1.0
O C:ACT402 4.4 45.2 1.0
CA C:HIS171 4.4 32.9 1.0
H C:HIS86 4.5 38.1 1.0
HG2 C:GLU89 4.5 42.5 1.0
OE2 C:GLU272 4.5 40.9 1.0
OH C:TYR88 4.5 56.3 1.0
HD22 C:ASN138 4.6 31.1 1.0
N C:GLU172 4.7 31.0 1.0
HE1 C:TYR88 4.7 55.8 1.0
CZ C:ARG129 4.7 50.6 1.0
C C:ACT402 4.8 46.9 1.0
CA C:HIS86 4.8 28.2 1.0
OE1 C:GLU272 4.8 31.4 1.0
HB2 C:GLU89 4.9 41.5 1.0
HH C:TYR88 4.9 67.6 1.0
N C:HIS86 4.9 31.8 1.0

Zinc binding site 4 out of 4 in 4oko

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Zinc binding site 4 out of 4 in the Crystal Structure of Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa)


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 Francisella Tularensis REP34 (Rapid Encystment Phenotype Protein 34 kDa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.1
occ:1.00
OE2 D:GLU89 2.1 29.6 1.0
ND1 D:HIS171 2.1 26.3 1.0
ND1 D:HIS86 2.2 30.0 1.0
O D:HOH501 2.5 25.8 1.0
OE1 D:GLU89 2.6 34.8 1.0
CD D:GLU89 2.7 31.4 1.0
HB3 D:HIS171 2.8 34.4 1.0
HB2 D:HIS86 3.0 35.5 1.0
CE1 D:HIS171 3.1 31.7 1.0
CE1 D:HIS86 3.1 28.9 1.0
CG D:HIS171 3.1 27.8 1.0
CG D:HIS86 3.2 28.9 1.0
HE1 D:HIS171 3.3 38.0 1.0
HE1 D:HIS86 3.3 34.7 1.0
CB D:HIS171 3.5 28.7 1.0
CB D:HIS86 3.5 29.5 1.0
O D:HOH542 3.6 31.7 1.0
HB3 D:HIS86 3.9 35.5 1.0
H D:GLU172 4.0 36.4 1.0
HH22 D:ARG129 4.0 71.0 1.0
HH21 D:ARG129 4.1 71.0 1.0
O D:HOH513 4.1 32.1 1.0
CG D:GLU89 4.1 35.6 1.0
HB2 D:HIS171 4.1 34.4 1.0
NH2 D:ARG129 4.1 59.2 1.0
HA D:HIS171 4.2 34.8 1.0
O D:GLU172 4.2 35.1 1.0
NE2 D:HIS171 4.2 28.9 1.0
NE2 D:HIS86 4.3 28.3 1.0
CD2 D:HIS171 4.3 27.4 1.0
H2 D:ACT402 4.3 55.2 1.0
CD2 D:HIS86 4.3 28.2 1.0
HG3 D:GLU89 4.4 42.7 1.0
CA D:HIS171 4.4 29.0 1.0
H D:HIS86 4.5 39.4 1.0
OH D:TYR88 4.5 51.6 1.0
O D:ACT402 4.5 41.8 1.0
HG2 D:GLU89 4.6 42.7 1.0
N D:GLU172 4.6 30.3 1.0
HD22 D:ASN138 4.7 36.5 1.0
C D:ACT402 4.7 46.1 1.0
HE1 D:TYR88 4.7 47.8 1.0
CZ D:ARG129 4.8 53.8 1.0
OE2 D:GLU272 4.8 35.3 1.0
CA D:HIS86 4.8 28.4 1.0
HH D:TYR88 4.9 62.0 1.0
HB2 D:GLU89 4.9 42.4 1.0
OE1 D:GLU272 4.9 32.5 1.0
N D:HIS86 5.0 32.9 1.0

Reference:

G.K.Feld, S.El-Etr, M.H.Corzett, M.S.Hunter, K.Belhocine, D.M.Monack, M.Frank, B.W.Segelke, A.Rasley. Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella Tularensis Host-Cell Invasion. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25231992
DOI: 10.1074/JBC.M114.599381
Page generated: Wed Dec 16 05:39:14 2020

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