Atomistry » Manganese » PDB 3n39-3orm » 3oly
Atomistry »
  Manganese »
    PDB 3n39-3orm »
      3oly »

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

Go back to Manganese Binding Sites List in 3oly
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

Go back to Manganese Binding Sites List in 3oly
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy