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Manganese in PDB 6sre: Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones

Enzymatic activity of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones

All present enzymatic activity of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones, PDB code: 6sre was solved by E.Wator, M.Rutkiewicz, P.Wilk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.77 / 1.39
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.725, 106.858, 216.323, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones (pdb code 6sre). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones, PDB code: 6sre:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6sre

Go back to Manganese Binding Sites List in 6sre
Manganese binding site 1 out of 4 in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:0.1
occ:1.00
H2 A:MH2506 1.4 21.0 0.5
OD2 A:ASP287 2.1 31.4 1.0
O1 A:MH2506 2.2 17.5 0.5
NE2 A:HIS370 2.3 16.9 1.0
OE2 A:GLU412 2.3 33.5 1.0
OE2 A:GLU452 2.3 31.1 1.0
O A:GLY507 2.5 39.4 1.0
H2 A:GLY507 3.0 44.1 1.0
CD A:GLU412 3.1 27.2 1.0
CG A:ASP287 3.1 25.9 1.0
C A:GLY507 3.2 37.9 1.0
MN A:MH2506 3.2 36.8 0.5
CE1 A:HIS370 3.2 17.6 1.0
HG1 A:THR410 3.2 19.5 1.0
CD2 A:HIS370 3.2 16.5 1.0
OE1 A:GLU412 3.3 24.7 1.0
CD A:GLU452 3.3 21.9 1.0
HG21 A:THR410 3.3 21.1 1.0
HE1 A:HIS370 3.4 21.1 1.0
HD2 A:HIS370 3.4 19.7 1.0
HA A:PRO508 3.6 40.6 1.0
OE1 A:GLU452 3.6 23.4 1.0
N A:GLY507 3.7 36.7 1.0
OD1 A:ASP287 3.8 26.4 1.0
HE2 A:HIS377 3.8 21.7 1.0
N A:PRO508 3.9 37.2 1.0
CA A:GLY507 3.9 40.0 1.0
HB3 A:ASP287 4.0 28.9 1.0
OG1 A:THR410 4.0 16.2 1.0
CA A:PRO508 4.2 33.9 1.0
CG2 A:THR410 4.2 17.6 1.0
CB A:ASP287 4.2 24.1 1.0
HA2 A:GLY507 4.2 48.0 1.0
H1 A:GLY507 4.2 44.1 1.0
HB A:THR410 4.2 20.2 1.0
H3 A:GLY507 4.3 44.1 1.0
ND1 A:HIS370 4.3 16.2 1.0
CG A:HIS370 4.4 16.8 1.0
CB A:THR410 4.4 16.9 1.0
HD2 A:HIS377 4.4 22.5 1.0
CG A:GLU412 4.5 17.9 1.0
HG13 A:VAL376 4.5 28.3 1.0
HG3 A:GLU452 4.5 22.1 1.0
NE2 A:HIS377 4.6 18.1 1.0
CG A:GLU452 4.6 18.4 1.0
HG2 A:GLU412 4.6 21.4 1.0
HG12 A:VAL376 4.6 28.3 1.0
HG23 A:THR410 4.6 21.1 1.0
HB2 A:ASP287 4.6 28.9 1.0
HD3 A:PRO508 4.7 49.0 1.0
HG22 A:THR410 4.8 21.1 1.0
HA3 A:GLY507 4.8 48.0 1.0
CD2 A:HIS377 4.9 18.8 1.0
HG11 A:VAL376 4.9 28.3 1.0
CG1 A:VAL376 4.9 23.6 1.0
HB3 A:GLU412 4.9 19.2 1.0
CD A:PRO508 4.9 40.8 1.0
C A:PRO508 4.9 30.6 1.0

Manganese binding site 2 out of 4 in 6sre

Go back to Manganese Binding Sites List in 6sre
Manganese binding site 2 out of 4 in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:36.8
occ:0.47
MN A:MH2506 0.0 36.8 0.5
O1 A:MH2506 2.0 17.5 0.5
OD1 A:ASP276 2.2 23.8 1.0
OD1 A:ASP287 2.3 26.4 1.0
OD2 A:ASP276 2.4 26.4 1.0
H1 A:GLY507 2.4 44.1 1.0
OE1 A:GLU452 2.4 23.4 1.0
H2 A:GLY507 2.4 44.1 1.0
CG A:ASP276 2.6 23.7 1.0
H2 A:MH2506 2.6 21.0 0.5
N A:GLY507 2.7 36.7 1.0
HA2 A:GLY507 2.8 48.0 1.0
CG A:ASP287 2.9 25.9 1.0
OD2 A:ASP287 3.0 31.4 1.0
CA A:GLY507 3.2 40.0 1.0
HG1 A:THR289 3.2 22.3 1.0
MN A:MN501 3.2 0.1 1.0
CD A:GLU452 3.3 21.9 1.0
OE2 A:GLU452 3.5 31.1 1.0
OG1 A:THR289 3.6 18.6 1.0
H3 A:GLY507 3.6 44.1 1.0
OH A:TYR241 3.6 94.9 1.0
C A:GLY507 3.7 37.9 1.0
HH A:TYR241 3.7 0.9 1.0
HD3 A:PRO508 3.9 49.0 1.0
O A:GLY507 4.0 39.4 1.0
OE1 A:GLU412 4.0 24.7 1.0
HA3 A:GLY507 4.1 48.0 1.0
CB A:ASP276 4.1 21.9 1.0
CZ A:TYR241 4.1 94.3 1.0
HE A:ARG450 4.1 22.6 1.0
HH21 A:ARG450 4.2 26.5 1.0
CB A:ASP287 4.3 24.1 1.0
HE2 A:TYR241 4.4 0.9 1.0
N A:PRO508 4.4 37.2 1.0
HB2 A:ASP276 4.4 26.3 1.0
HD12 A:ILE244 4.4 52.3 1.0
CE2 A:TYR241 4.5 94.1 1.0
HB3 A:ASP276 4.5 26.3 1.0
HA A:ASP276 4.6 21.3 1.0
CD A:PRO508 4.6 40.8 1.0
HB3 A:ASP287 4.7 28.9 1.0
HA A:ASP287 4.7 24.0 1.0
C A:ASP287 4.7 18.5 1.0
CG A:GLU452 4.7 18.4 1.0
N A:ILE288 4.8 17.5 1.0
OE2 A:GLU412 4.8 33.5 1.0
CD A:GLU412 4.8 27.2 1.0
HB3 A:GLU452 4.8 19.8 1.0
H A:ILE288 4.8 21.0 1.0
CA A:ASP276 4.8 17.8 1.0
O A:ILE288 4.8 19.5 1.0
CA A:ASP287 4.8 20.0 1.0
HB2 A:GLU452 4.8 19.8 1.0
CE1 A:TYR241 4.9 94.0 1.0
NE A:ARG450 4.9 18.9 1.0
HB2 A:ASP287 4.9 28.9 1.0
C A:ILE288 4.9 17.4 1.0
CB A:THR289 5.0 17.1 1.0
NH2 A:ARG450 5.0 22.1 1.0

Manganese binding site 3 out of 4 in 6sre

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Manganese binding site 3 out of 4 in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:20.6
occ:0.77
OD2 B:ASP287 2.1 27.6 1.0
OE2 B:GLU452 2.3 22.1 1.0
O1 B:MH2502 2.3 18.3 0.5
NE2 B:HIS370 2.3 16.5 1.0
OE2 B:GLU412 2.3 22.1 1.0
O B:GLY508 2.5 29.4 1.0
H2 B:GLY508 3.0 44.3 1.0
CD B:GLU412 3.1 21.0 1.0
CG B:ASP287 3.1 26.9 1.0
H2 B:MH2502 3.2 21.9 0.5
HG21 B:THR410 3.2 20.6 1.0
MN B:MH2502 3.2 30.5 0.5
HG1 B:THR410 3.2 19.8 1.0
C B:GLY508 3.3 30.9 1.0
OE1 B:GLU412 3.3 23.2 1.0
CD B:GLU452 3.3 21.7 1.0
CD2 B:HIS370 3.3 14.7 1.0
CE1 B:HIS370 3.3 15.4 1.0
HD2 B:HIS370 3.4 17.6 1.0
HE1 B:HIS370 3.5 18.5 1.0
HA B:PRO509 3.6 31.6 1.0
OE1 B:GLU452 3.6 22.4 1.0
N B:GLY508 3.8 36.9 1.0
OD1 B:ASP287 3.8 28.3 1.0
HE2 B:HIS377 3.9 22.0 1.0
N B:PRO509 4.0 30.4 1.0
HB3 B:ASP287 4.0 28.0 1.0
CA B:GLY508 4.0 35.9 1.0
H1 B:GLY508 4.0 44.3 1.0
OG1 B:THR410 4.0 16.5 1.0
CG2 B:THR410 4.1 17.2 1.0
CB B:ASP287 4.2 23.4 1.0
CA B:PRO509 4.2 26.3 1.0
HB B:THR410 4.2 19.2 1.0
HA2 B:GLY508 4.3 43.0 1.0
CB B:THR410 4.4 16.0 1.0
ND1 B:HIS370 4.4 15.8 1.0
CG B:HIS370 4.4 14.8 1.0
H3 B:GLY508 4.4 44.3 1.0
HD2 B:HIS377 4.5 21.0 1.0
CG B:GLU412 4.5 18.9 1.0
HG23 B:THR410 4.5 20.6 1.0
HG12 B:VAL376 4.5 25.9 1.0
HG3 B:GLU452 4.6 22.7 1.0
HG13 B:VAL376 4.6 25.9 1.0
CG B:GLU452 4.6 18.9 1.0
NE2 B:HIS377 4.6 18.4 1.0
HG2 B:GLU412 4.6 22.7 1.0
HB2 B:ASP287 4.6 28.0 1.0
HG22 B:THR410 4.7 20.6 1.0
HG11 B:VAL376 4.8 25.9 1.0
HB3 B:GLU412 4.8 20.9 1.0
HA3 B:GLY508 4.9 43.0 1.0
CG1 B:VAL376 4.9 21.6 1.0
CD2 B:HIS377 4.9 17.5 1.0
HD3 B:PRO509 4.9 38.8 1.0
C B:PRO509 5.0 26.9 1.0

Manganese binding site 4 out of 4 in 6sre

Go back to Manganese Binding Sites List in 6sre
Manganese binding site 4 out of 4 in the Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Prolidase S202F Variant Expressed in the Presence of Chaperones within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:30.5
occ:0.51
MN B:MH2502 0.0 30.5 0.5
O1 B:MH2502 2.0 18.3 0.5
OD1 B:ASP276 2.2 22.9 1.0
H1 B:GLY508 2.2 44.3 1.0
OD2 B:ASP276 2.3 23.6 1.0
OE1 B:GLU452 2.3 22.4 1.0
OD1 B:ASP287 2.4 28.3 1.0
CG B:ASP276 2.5 23.6 1.0
H2 B:MH2502 2.6 21.9 0.5
H2 B:GLY508 2.7 44.3 1.0
N B:GLY508 2.8 36.9 1.0
HA2 B:GLY508 2.9 43.0 1.0
CG B:ASP287 3.0 26.9 1.0
OD2 B:ASP287 3.1 27.6 1.0
HG1 B:THR289 3.1 22.4 1.0
HH B:TYR241 3.1 0.2 1.0
CD B:GLU452 3.2 21.7 1.0
MN B:MN501 3.2 20.6 0.8
CA B:GLY508 3.3 35.9 1.0
OE2 B:GLU452 3.4 22.1 1.0
OH B:TYR241 3.5 93.5 1.0
OG1 B:THR289 3.5 18.7 1.0
H3 B:GLY508 3.6 44.3 1.0
C B:GLY508 3.8 30.9 1.0
OE1 B:GLU412 3.9 23.2 1.0
O B:GLY508 4.0 29.4 1.0
HE1 B:TYR241 4.0 0.4 1.0
CB B:ASP276 4.0 20.4 1.0
HD3 B:PRO509 4.0 38.8 1.0
HE B:ARG450 4.1 24.4 1.0
HA3 B:GLY508 4.2 43.0 1.0
CZ B:TYR241 4.2 92.3 1.0
HH21 B:ARG450 4.3 26.6 1.0
CB B:ASP287 4.4 23.4 1.0
CE1 B:TYR241 4.4 92.0 1.0
HB2 B:ASP276 4.4 24.5 1.0
N B:PRO509 4.5 30.4 1.0
HB3 B:ASP276 4.5 24.5 1.0
HD12 B:ILE244 4.5 42.6 1.0
HA B:ASP276 4.6 22.2 1.0
CG B:GLU452 4.6 18.9 1.0
C B:ASP287 4.7 17.4 1.0
HB3 B:ASP287 4.7 28.0 1.0
CD B:PRO509 4.7 32.4 1.0
HB3 B:GLU452 4.7 21.0 1.0
CD B:GLU412 4.7 21.0 1.0
HA B:ASP287 4.7 21.4 1.0
OE2 B:GLU412 4.8 22.1 1.0
CA B:ASP276 4.8 18.5 1.0
N B:ILE288 4.8 17.1 1.0
HB2 B:GLU452 4.8 21.0 1.0
H B:ILE288 4.8 20.4 1.0
NE B:ARG450 4.8 20.4 1.0
CA B:ASP287 4.8 17.9 1.0
O B:ILE288 4.9 17.9 1.0
CB B:THR289 4.9 17.4 1.0
C B:ILE288 5.0 16.9 1.0
HB2 B:ASP287 5.0 28.0 1.0
NH2 B:ARG450 5.0 22.2 1.0
CB B:GLU452 5.0 17.5 1.0

Reference:

E.Wator, M.Rutkiewicz, M.S.Weiss, P.Wilk. Co-Expression with Chaperones Can Affect Protein 3D-Structure As Exemplified By Loss-of-Function Variants of Human Prolidase. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 32598484
DOI: 10.1002/1873-3468.13877
Page generated: Tue Dec 15 05:01:48 2020

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