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Manganese in PDB 5hzz: Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese

Protein crystallography data

The structure of Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese, PDB code: 5hzz was solved by C.S.Mota, A.M.D.Goncalves, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.452, 77.893, 52.597, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese (pdb code 5hzz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese, PDB code: 5hzz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5hzz

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Manganese binding site 1 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


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 DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:22.2
occ:0.71
 O A:HOH414 2.1 21.7 1.0
OD2 A:ASP82 2.2 17.4 1.0
OE1 A:GLU79 2.2 22.2 1.0
O A:HOH418 2.3 41.3 1.0
O A:HOH315 2.4 36.7 1.0
CD A:GLU79 3.2 28.8 1.0
CG A:ASP82 3.2 19.4 1.0
OE2 A:GLU79 3.5 31.5 1.0
OE2 A:GLU50 3.5 56.4 1.0
CB A:ASP82 3.6 13.2 1.0
O A:HOH364 4.1 14.1 1.0
OD1 A:ASP82 4.3 13.0 1.0
O A:HOH475 4.4 28.5 1.0
CD A:GLU50 4.4 47.1 1.0
CG A:GLU79 4.6 17.7 1.0
CG A:GLU50 4.6 20.7 1.0
CA A:GLU79 4.7 12.2 1.0
O A:HOH437 4.7 37.5 1.0
CB A:GLU50 4.9 16.5 1.0
CB A:GLU79 5.0 13.3 1.0

Manganese binding site 2 out of 6 in 5hzz

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Manganese binding site 2 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


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 DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:21.4
occ:0.72
 O B:HOH1007 2.1 36.2 1.0
OD2 B:ASP82 2.2 21.8 1.0
OE1 B:GLU79 2.2 22.0 1.0
O B:HOH1035 2.3 23.3 1.0
O B:HOH952 2.4 32.8 1.0
O B:HOH1045 2.4 36.9 1.0
CD B:GLU79 3.2 27.9 1.0
CG B:ASP82 3.2 24.2 1.0
OE2 B:GLU79 3.4 33.3 1.0
CB B:ASP82 3.6 17.6 1.0
O B:HOH968 4.1 15.5 1.0
OD1 B:ASP82 4.3 20.1 1.0
O B:HOH1066 4.3 39.6 1.0
O B:HOH1093 4.5 29.8 1.0
O B:HOH1053 4.5 41.3 1.0
CG B:GLU79 4.6 17.9 1.0
CG B:GLU50 4.6 28.5 1.0
O B:HOH903 4.7 48.4 1.0
CB B:GLU50 4.7 17.6 1.0
CA B:GLU79 4.7 14.9 1.0
CB B:GLU79 4.9 17.3 1.0
O B:HOH961 5.0 24.1 1.0

Manganese binding site 3 out of 6 in 5hzz

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Manganese binding site 3 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


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 DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:15.3
occ:0.78
 O C:HOH385 2.1 25.8 1.0
O C:HOH434 2.1 28.8 1.0
OE2 C:GLU50 2.2 19.1 1.0
OP2 C:UMP201 2.2 12.2 1.0
OE2 C:GLU46 2.3 26.3 1.0
O C:HOH401 2.5 26.5 1.0
CD C:GLU50 3.1 25.1 1.0
CD C:GLU46 3.1 29.6 1.0
OE1 C:GLU50 3.4 26.5 1.0
P C:UMP201 3.4 15.9 1.0
OP3 C:UMP201 3.6 15.9 1.0
CG C:GLU46 3.6 25.1 1.0
MN C:MN203 3.7 22.6 0.5
O C:HOH359 4.0 34.0 1.0
O C:HOH443 4.0 42.9 1.0
OE1 C:GLU46 4.1 21.0 1.0
NZ A:LYS122 4.1 12.5 1.0
C5' C:UMP201 4.2 13.0 1.0
O C:HOH446 4.3 22.9 1.0
O5' C:UMP201 4.3 14.9 1.0
O D:HOH399 4.3 27.7 1.0
CG C:GLU50 4.5 14.6 1.0
OP1 C:UMP201 4.5 14.6 1.0
CB C:GLU46 5.0 18.2 1.0

Manganese binding site 4 out of 6 in 5hzz

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Manganese binding site 4 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


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 DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn203

b:22.6
occ:0.52
 OE1 C:GLU50 2.0 26.5 1.0
OD2 C:ASP82 2.2 20.6 1.0
OE1 C:GLU79 2.5 20.3 1.0
O C:HOH385 2.7 25.8 1.0
O C:HOH401 2.9 26.5 1.0
O C:HOH383 3.0 18.7 1.0
CD C:GLU50 3.0 25.1 1.0
CG C:ASP82 3.1 19.4 1.0
CB C:ASP82 3.2 10.1 1.0
O C:HOH327 3.4 23.8 1.0
OE2 C:GLU50 3.6 19.1 1.0
CD C:GLU79 3.6 27.4 1.0
MN C:MN202 3.7 15.3 0.8
O C:HOH443 3.8 42.9 1.0
OE2 C:GLU79 4.1 32.1 1.0
CG C:GLU50 4.1 14.6 1.0
OD1 C:ASP82 4.2 12.7 1.0
CB C:GLU50 4.2 14.4 1.0
C5' C:UMP201 4.6 13.0 1.0
CA C:ALA47 4.7 11.6 1.0
CA C:GLU79 4.7 7.5 1.0
CA C:ASP82 4.8 10.4 1.0
C3' C:UMP201 4.9 10.7 1.0
CG C:GLU79 4.9 18.2 1.0
CB C:ALA47 4.9 13.4 1.0
O C:HOH446 5.0 22.9 1.0
CB C:GLU79 5.0 13.3 1.0
OP3 C:UMP201 5.0 15.9 1.0

Manganese binding site 5 out of 6 in 5hzz

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Manganese binding site 5 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:12.4
occ:0.67
 OE2 D:GLU50 2.1 25.0 1.0
OP3 D:UMP201 2.2 12.8 1.0
O D:HOH427 2.2 27.8 1.0
OE1 D:GLU46 2.2 10.9 0.6
O D:HOH366 2.3 26.1 1.0
O D:HOH396 2.4 20.5 1.0
CD D:GLU50 3.0 27.7 1.0
CD D:GLU46 3.0 12.3 0.6
OE1 D:GLU50 3.2 24.2 1.0
P D:UMP201 3.4 12.2 1.0
CG D:GLU46 3.5 9.7 0.6
OP1 D:UMP201 3.5 13.8 1.0
O D:HOH440 3.7 35.9 1.0
MN D:MN203 3.7 26.6 0.7
O D:HOH318 3.8 31.2 1.0
OE2 D:GLU46 4.0 14.5 0.6
NZ B:LYS122 4.1 11.1 1.0
C5' D:UMP201 4.2 10.7 1.0
O D:HOH367 4.2 27.5 1.0
O D:HOH450 4.3 24.7 1.0
O5' D:UMP201 4.3 12.0 1.0
CG D:GLU50 4.4 13.2 1.0
OP2 D:UMP201 4.5 9.9 1.0
OE1 D:GLU46 4.6 14.6 0.5
CB D:GLU46 4.8 10.3 0.6
CB D:GLU46 4.8 10.3 0.5

Manganese binding site 6 out of 6 in 5hzz

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Manganese binding site 6 out of 6 in the Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of DR2231_E47A Mutant in Complex with Dump and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn203

b:26.6
occ:0.72
 OE1 D:GLU50 2.0 24.2 1.0
OD2 D:ASP82 2.4 20.6 1.0
OE1 D:GLU79 2.5 16.5 1.0
O D:HOH366 2.6 26.1 1.0
O D:HOH363 2.9 18.2 1.0
O D:HOH396 3.0 20.5 1.0
CD D:GLU50 3.0 27.7 1.0
CG D:ASP82 3.2 16.2 1.0
CB D:ASP82 3.3 11.2 1.0
O D:HOH440 3.4 35.9 1.0
CD D:GLU79 3.6 26.3 1.0
O D:HOH387 3.6 21.2 1.0
OE2 D:GLU50 3.6 25.0 1.0
MN D:MN202 3.7 12.4 0.7
CG D:GLU50 4.1 13.2 1.0
CB D:GLU50 4.1 12.2 1.0
OE2 D:GLU79 4.2 37.5 1.0
OD1 D:ASP82 4.3 12.6 1.0
CA D:ALA47 4.5 9.9 1.0
C5' D:UMP201 4.5 10.7 1.0
CA D:GLU79 4.7 9.8 1.0
O D:HOH450 4.8 24.7 1.0
CA D:ASP82 4.8 11.9 1.0
CG D:GLU79 4.8 14.7 1.0
CB D:ALA47 4.9 11.8 1.0
CB D:GLU79 4.9 12.3 1.0
OP3 D:UMP201 4.9 12.8 1.0
OP1 D:UMP201 4.9 13.8 1.0
C3' D:UMP201 4.9 12.7 1.0

Reference:

C.S.Mota, A.M.Goncalves, D.De Sanctis. Deinococcus Radiodurans DR2231 Is A Two-Metal-Ion Mechanism Hydrolase with Exclusive Activity on Dutp. Febs J. V. 283 4274 2016.
ISSN: ISSN 1742-4658
PubMed: 27739259
DOI: 10.1111/FEBS.13923
Page generated: Sun Oct 6 01:27:03 2024

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