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Manganese in PDB 3oly: Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex

Protein crystallography data

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex, PDB code: 3oly was solved by R.M.Immormino, R.B.Bourret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.72 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.445, 53.547, 161.082, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.2

Other elements in 3oly:

The structure of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex (pdb code 3oly). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex, PDB code: 3oly:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3oly

Go back to Manganese Binding Sites List in 3oly
Manganese binding site 1 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn131

b:30.1
occ:1.00
 OD2 A:ASP57 2.1 22.7 1.0
O A:HOH137 2.1 27.9 1.0
OD1 A:ASP13 2.2 31.3 1.0
F2 A:BEF130 2.2 32.7 1.0
O A:ASN59 2.3 26.2 1.0
O A:HOH138 2.3 27.2 1.0
CG A:ASP57 3.1 29.0 1.0
CG A:ASP13 3.2 34.1 1.0
BE A:BEF130 3.3 34.9 1.0
OD1 A:ASP57 3.4 26.9 1.0
C A:ASN59 3.4 37.8 1.0
OD2 A:ASP13 3.5 36.3 1.0
OD1 A:ASP12 3.9 28.8 1.0
CB A:ASN59 4.1 30.4 1.0
CA A:ASN59 4.1 29.9 1.0
F1 A:BEF130 4.2 27.7 1.0
O A:HOH179 4.2 52.2 1.0
CG A:MET60 4.2 25.2 1.0
N A:ASN59 4.3 29.7 1.0
F3 A:BEF130 4.3 27.3 1.0
CD2 A:PHE14 4.3 38.8 1.0
N A:ASP13 4.4 28.0 1.0
CB A:ASP57 4.4 25.4 1.0
O A:HOH281 4.4 48.5 1.0
CG A:ASP12 4.5 30.8 1.0
N A:MET60 4.5 26.0 1.0
CB A:ASP13 4.5 30.4 1.0
NZ A:LYS109 4.6 33.3 1.0
OD2 A:ASP12 4.6 29.4 1.0
O A:HOH285 4.7 50.6 1.0
CE2 A:PHE14 4.7 50.7 1.0
CA A:MET60 4.8 27.0 1.0
CA A:ASP13 4.9 31.2 1.0

Manganese binding site 2 out of 6 in 3oly

Go back to Manganese Binding Sites List in 3oly
Manganese binding site 2 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn132

b:91.4
occ:1.00
 OG A:SER15 2.5 46.2 0.5
CB A:SER15 3.4 45.2 0.5
O A:HOH189 3.5 53.1 1.0
N A:SER15 3.6 38.0 0.5
N A:SER15 3.6 38.0 0.5
CB A:SER15 3.7 45.6 0.5
O A:HOH186 3.8 53.6 1.0
CA A:SER15 4.1 40.6 0.5
CA A:SER15 4.3 40.5 0.5
O A:HOH290 4.3 63.8 1.0
C A:PHE14 4.6 37.8 1.0
CA A:PHE14 4.6 34.4 1.0
O A:HOH165 4.7 52.9 1.0
O A:ASP13 4.7 43.9 1.0
CD1 A:PHE14 4.7 55.2 1.0
OG A:SER15 4.9 45.5 0.5

Manganese binding site 3 out of 6 in 3oly

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Manganese binding site 3 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn133

b:0.2
occ:1.00
 N A:GLY50 3.4 43.7 1.0
CA A:GLY49 4.0 42.8 1.0
O A:HOH277 4.2 61.4 1.0
C A:GLY49 4.2 45.4 1.0
CA A:GLY50 4.3 45.5 1.0
O A:HOH185 4.4 54.4 1.0
O A:HOH252 4.7 45.6 1.0

Manganese binding site 4 out of 6 in 3oly

Go back to Manganese Binding Sites List in 3oly
Manganese binding site 4 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn131

b:33.7
occ:1.00
 OD2 B:ASP57 2.1 26.1 1.0
O B:HOH139 2.2 30.7 1.0
F2 B:BEF130 2.2 30.1 1.0
O B:ASN59 2.2 31.3 1.0
OD1 B:ASP13 2.2 32.1 1.0
O B:HOH142 2.4 30.5 1.0
CG B:ASP57 3.1 30.4 1.0
CG B:ASP13 3.2 33.9 1.0
BE B:BEF130 3.4 35.0 1.0
C B:ASN59 3.4 37.5 1.0
OD1 B:ASP57 3.5 25.8 1.0
OD2 B:ASP13 3.5 37.6 1.0
O B:HOH209 3.9 45.2 1.0
OD1 B:ASP12 4.0 30.3 1.0
CB B:ASN59 4.0 34.7 0.5
CB B:ASN59 4.1 34.8 0.5
CA B:ASN59 4.1 34.1 0.5
CA B:ASN59 4.1 34.1 0.5
F1 B:BEF130 4.2 31.2 1.0
F3 B:BEF130 4.3 30.4 1.0
CG B:MET60 4.3 25.0 1.0
CD2 B:PHE14 4.3 44.4 1.0
N B:ASN59 4.3 30.7 1.0
O B:HOH227 4.3 48.3 1.0
CB B:ASP57 4.5 26.1 1.0
N B:MET60 4.5 31.3 1.0
N B:ASP13 4.5 28.0 1.0
CB B:ASP13 4.5 30.3 1.0
O B:HOH271 4.6 57.8 1.0
O B:HOH184 4.6 53.6 1.0
CG B:ASP12 4.6 30.8 1.0
CE2 B:PHE14 4.6 45.3 1.0
CA B:MET60 4.7 30.1 1.0
NZ B:LYS109 4.7 32.4 1.0
OD2 B:ASP12 4.8 34.1 1.0
CG B:ASN59 4.8 38.2 0.5
CA B:ASP13 5.0 32.5 1.0

Manganese binding site 5 out of 6 in 3oly

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Manganese binding site 5 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn132

b:89.1
occ:1.00
 O B:HOH275 3.2 59.5 1.0
O B:HOH170 3.5 52.4 1.0
N B:SER15 3.6 39.7 1.0
O B:HOH156 3.7 51.3 1.0
CB B:SER15 3.8 49.4 1.0
O B:HOH305 3.8 64.0 1.0
O B:HOH249 4.1 54.5 1.0
CA B:SER15 4.3 41.5 1.0
O B:ASP13 4.3 39.8 1.0
CA B:PHE14 4.3 41.1 1.0
C B:PHE14 4.5 36.2 1.0
CD1 B:PHE14 4.6 61.2 1.0

Manganese binding site 6 out of 6 in 3oly

Go back to Manganese Binding Sites List in 3oly
Manganese binding site 6 out of 6 in the Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structural and Functional Effects of Substitution at Position T+1 in Chey: CHEYA88M-BEF3-Mn Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn133

b:75.2
occ:1.00
 O A:HOH263 3.3 47.6 1.0
N B:LYS92 3.4 38.2 1.0
NZ A:LYS92 3.5 43.9 1.0
O A:HOH230 3.6 57.2 1.0
O B:HOH206 3.8 45.4 1.0
CB B:LYS92 3.9 35.5 1.0
CA B:LYS91 4.0 42.5 1.0
C B:LYS91 4.2 40.6 1.0
CA B:LYS92 4.3 38.6 1.0
CG B:LYS91 4.4 52.4 1.0
CB B:LYS91 4.5 46.0 1.0
O B:HOH232 4.6 57.4 1.0
O B:ALA90 4.8 41.8 1.0
O A:HOH145 5.0 50.6 1.0
O B:HOH205 5.0 46.4 1.0
CE A:LYS92 5.0 46.5 1.0

Reference:

R.M.Immormino, R.E.Silversmith, R.B.Bourret. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation. Biochemistry V. 55 5595 2016.
ISSN: ISSN 0006-2960
PubMed: 27589219
DOI: 10.1021/ACS.BIOCHEM.6B00645
Page generated: Sat Oct 5 17:24:46 2024

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