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Platinum in PDB 5dlb: Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M

Protein crystallography data

The structure of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M, PDB code: 5dlb was solved by S.Chan, M.A.Arbing, J.Kim, S.Kahng, M.R.Sawaya, D.S.Eisenberg, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.96 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.206, 46.019, 58.006, 90.00, 92.24, 90.00
R / Rfree (%) 20.9 / 24.5

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M (pdb code 5dlb). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 7 binding sites of Platinum where determined in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M, PDB code: 5dlb:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7;

Platinum binding site 1 out of 7 in 5dlb

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Platinum binding site 1 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt306

b:56.4
occ:1.00
S A:SCN307 2.3 61.5 1.0
S A:SCN311 2.5 67.2 1.0
S A:SCN310 2.6 65.0 1.0
S A:SCN312 2.7 65.7 1.0
C A:SCN307 2.8 62.0 1.0
S A:SCN308 2.9 63.2 1.0
S A:SCN309 2.9 84.9 1.0
C A:SCN308 3.0 62.3 1.0
C A:SCN311 3.1 68.0 1.0
C A:SCN312 3.2 54.9 1.0
C A:SCN310 3.3 65.0 1.0
N A:SCN307 3.5 47.0 1.0
N A:SCN308 3.6 55.6 1.0
N A:SCN311 3.8 55.4 1.0
N A:SCN312 4.0 51.5 1.0
N A:SCN310 4.0 58.6 1.0
C A:SCN309 4.4 95.1 1.0

Platinum binding site 2 out of 7 in 5dlb

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Platinum binding site 2 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt313

b:57.5
occ:0.90
S A:SCN314 2.2 65.6 1.0
S A:SCN316 2.3 65.9 1.0
S A:SCN318 2.4 71.9 1.0
S A:SCN317 2.7 70.5 1.0
S A:SCN315 2.8 85.9 1.0
S A:SCN319 2.8 76.3 1.0
C A:SCN318 3.0 76.5 1.0
C A:SCN317 3.1 52.8 1.0
C A:SCN314 3.2 48.7 1.0
C A:SCN316 3.3 69.1 1.0
C A:SCN315 3.7 83.6 1.0
N A:SCN317 3.8 57.5 1.0
C A:SCN319 3.8 77.8 1.0
N A:SCN318 3.9 75.7 1.0
N A:SCN314 4.2 56.3 1.0
N A:SCN316 4.3 59.5 1.0
OG A:SER257 4.6 38.1 1.0
N A:SCN315 4.7 75.4 1.0
N A:SCN319 4.8 73.2 1.0
CG A:MET170 4.9 41.0 1.0

Platinum binding site 3 out of 7 in 5dlb

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Platinum binding site 3 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt320

b:55.5
occ:0.74
S A:SCN321 2.3 66.1 1.0
SD A:MET170 2.4 45.0 1.0
S A:SCN322 2.6 90.0 1.0
C A:SCN322 3.3 86.6 1.0
CG A:MET170 3.8 41.0 1.0
C A:SCN321 3.8 48.4 1.0
CB A:MET170 3.8 40.1 1.0
CE A:MET170 4.0 44.2 1.0
N A:SCN322 4.1 92.9 1.0
CB A:GLU254 4.5 46.8 1.0
CA A:GLU254 4.6 46.0 1.0
N A:TRP255 4.7 42.4 1.0
CG A:ARG171 4.8 46.2 1.0
N A:SCN321 4.9 56.3 1.0
C A:MET170 5.0 38.6 1.0
CA A:MET170 5.0 37.9 1.0

Platinum binding site 4 out of 7 in 5dlb

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Platinum binding site 4 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt323

b:88.5
occ:1.00
S A:SCN324 2.4 81.9 1.0
C A:SCN324 2.6 65.4 1.0
S A:SCN326 2.8 79.4 1.0
C A:SCN327 3.0 78.7 1.0
N A:SCN324 3.2 67.1 1.0
S A:SCN327 3.2 85.1 1.0
S A:SCN325 3.2 82.2 1.0
C A:SCN326 3.3 62.3 1.0
N A:SCN327 3.3 78.3 1.0
C A:SCN328 3.6 98.7 1.0
C A:SCN325 3.6 72.9 1.0
S A:SCN328 3.8 0.2 1.0
N A:SCN328 3.8 86.5 1.0
N A:SCN326 4.0 62.7 1.0
N A:SCN325 4.2 64.0 1.0

Platinum binding site 5 out of 7 in 5dlb

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Platinum binding site 5 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt329

b:96.6
occ:1.00
C A:SCN331 2.9 67.5 1.0
S A:SCN331 2.9 73.4 1.0
S A:SCN330 3.0 86.4 1.0
N A:SCN331 3.3 71.2 1.0
S A:SCN333 3.4 89.2 1.0
S A:SCN332 3.6 72.4 1.0
C A:SCN333 4.0 80.0 1.0
C A:SCN330 4.1 84.4 1.0
C A:SCN332 4.4 65.4 1.0
N A:SCN333 4.7 74.8 1.0
OG A:SER182 4.7 44.4 1.0

Platinum binding site 6 out of 7 in 5dlb

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Platinum binding site 6 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt334

b:0.2
occ:1.00
S A:SCN338 2.8 75.8 1.0
S A:SCN336 3.1 95.6 1.0
C A:SCN336 3.1 95.3 1.0
S A:SCN337 3.2 73.4 1.0
C A:SCN335 3.2 88.4 1.0
S A:SCN335 3.2 87.3 1.0
N A:SCN336 3.4 88.5 1.0
C A:SCN337 3.6 77.8 1.0
N A:SCN335 3.6 85.0 1.0
C A:SCN338 3.7 71.7 1.0
N A:SCN337 4.3 72.7 1.0
N A:SCN338 4.6 63.8 1.0

Platinum binding site 7 out of 7 in 5dlb

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Platinum binding site 7 out of 7 in the Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Crystal Structure of Chaperone ESPG3 of Esx-3 Type VII Secretion System From Mycobacterium Marinum M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt339

b:0.0
occ:1.00
S A:SCN340 2.8 79.7 1.0
S A:SCN342 3.2 98.3 1.0
S A:SCN341 3.2 0.2 1.0
C A:SCN344 3.4 98.6 1.0
N A:SCN344 3.6 89.6 1.0
S A:SCN344 3.7 95.3 1.0
C A:SCN340 3.8 75.4 1.0
S A:SCN343 4.1 80.3 1.0
C A:SCN341 4.2 97.9 1.0
C A:SCN342 4.3 83.5 1.0
N A:SCN340 4.8 68.4 1.0

Reference:

A.T.Tuukkanen, D.Freire, S.Chan, M.A.Arbing, R.W.Reed, T.J.Evans, G.Zenkeviciute, J.Kim, S.Kahng, M.R.Sawaya, C.T.Chaton, M.Wilmanns, D.Eisenberg, A.H.A.Parret, K.V.Korotkov. Structural Variability of Espg Chaperones From Mycobacterial Esx-1, Esx-3, and Esx-5 Type VII Secretion Systems. J. Mol. Biol. V. 431 289 2019.
ISSN: ESSN 1089-8638
PubMed: 30419243
DOI: 10.1016/J.JMB.2018.11.003
Page generated: Wed Dec 16 02:05:13 2020

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