Atomistry » Manganese » PDB 1xif-1ytm » 1y63
Atomistry »
  Manganese »
    PDB 1xif-1ytm »
      1y63 »

Manganese in PDB 1y63: Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin

Protein crystallography data

The structure of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin, PDB code: 1y63 was solved by M.A.Robien, W.G.J.Hol, Structural Genomics Of Pathogenic Protozoaconsortium (Sgpp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.70
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.116, 107.116, 35.216, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.6

Other elements in 1y63:

The structure of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin also contains other interesting chemical elements:

Bromine (Br) 5 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin (pdb code 1y63). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin, PDB code: 1y63:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 1 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:12.9
occ:1.00
 O3B A:ADP301 2.1 12.1 1.0
OG1 A:THR24 2.1 19.2 1.0
O A:HOH1005 2.1 15.5 1.0
O A:HOH1008 2.2 16.2 1.0
O A:HOH1014 2.2 17.5 1.0
O A:HOH1013 2.2 17.3 1.0
CB A:THR24 3.2 18.6 1.0
PB A:ADP301 3.3 13.6 1.0
O1B A:ADP301 3.6 13.6 1.0
N A:THR24 4.0 17.1 1.0
O2A A:ADP301 4.1 14.8 1.0
CA A:THR24 4.2 16.9 1.0
CG2 A:THR24 4.2 21.7 1.0
OD1 A:ASP89 4.3 22.2 1.0
OD2 A:ASP89 4.3 21.9 1.0
OE2 A:GLU41 4.3 24.6 1.0
O3A A:ADP301 4.4 11.8 1.0
O2B A:ADP301 4.4 12.3 1.0
O A:HOH1001 4.6 13.7 1.0
PA A:ADP301 4.6 14.0 1.0
O A:HOH1080 4.6 34.2 1.0
CG A:ASP89 4.7 19.2 1.0
O A:HOH1010 4.8 16.7 1.0
O A:HOH1149 4.8 47.2 1.0
O1A A:ADP301 4.9 13.6 1.0
BR A:BR401 4.9 18.1 0.6
CE A:LYS23 4.9 17.3 1.0
CD A:GLU41 5.0 23.9 1.0

Manganese binding site 2 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 2 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn311

b:19.4
occ:1.00
 O A:HOH1038 2.0 23.9 1.0
OE2 A:GLU28 2.2 21.7 1.0
O A:HOH1030 2.2 22.9 1.0
O A:HOH1026 2.2 20.9 1.0
O A:HOH1031 2.3 22.8 1.0
ND1 A:HIS39 2.3 19.5 1.0
CD A:GLU28 3.1 24.3 1.0
CE1 A:HIS39 3.2 20.7 1.0
CG A:HIS39 3.3 21.5 1.0
OE1 A:GLU28 3.4 24.7 1.0
CB A:HIS39 3.7 22.9 1.0
O A:HOH1045 4.0 25.1 1.0
NE2 A:HIS39 4.3 19.6 1.0
CG A:GLU28 4.3 17.2 1.0
O A:HOH1086 4.4 34.9 1.0
CD2 A:HIS39 4.4 19.7 1.0
OE1 A:GLU41 4.5 25.4 1.0
O A:HIS39 4.5 22.1 1.0
O A:HOH1027 4.6 22.0 1.0
CA A:HIS39 4.9 20.7 1.0
C A:HIS39 4.9 20.1 1.0

Manganese binding site 3 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 3 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn351

b:15.3
occ:0.40
 O A:HOH1137 2.0 44.6 1.0
O A:HOH1111 2.0 39.1 1.0
O A:HOH1132 2.1 43.6 1.0
OD1 A:ASP70 2.1 27.7 1.0
O A:HOH1087 2.1 35.2 1.0
CG A:ASP70 3.1 25.4 1.0
OD2 A:ASP70 3.4 27.3 1.0
O A:HOH1146 3.9 46.1 1.0
CG A:GLU66 4.0 32.8 0.5
OE2 A:GLU66 4.1 38.7 0.5
O A:GLU66 4.3 24.6 1.0
CB A:ASP70 4.5 20.7 1.0
CD A:GLU66 4.5 35.7 0.5
CA A:ASP70 4.8 22.8 1.0
N A:ASP70 4.9 21.2 1.0

Manganese binding site 4 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 4 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn352

b:17.0
occ:0.30
 O A:HOH1117 2.1 39.6 1.0
OE1 A:GLU125 2.1 21.5 1.0
O A:HOH1130 2.2 42.3 1.0
CD A:GLU125 3.0 24.3 1.0
OE2 A:GLU125 3.3 23.4 1.0
CG A:GLU125 4.4 17.2 1.0
N A:GLU125 4.6 24.2 1.0
CB A:GLU125 4.8 16.2 1.0

Manganese binding site 5 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 5 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn353

b:12.3
occ:0.50
 O A:HOH1002 1.3 11.5 0.2
OE2 A:GLU98 2.3 18.1 1.0
O A:ALA147 2.7 32.2 1.0
CD A:GLU98 3.3 19.7 1.0
C A:ALA147 3.4 25.0 1.0
CA A:ALA147 3.7 22.2 1.0
O A:HOH1043 3.8 25.6 1.0
CG A:GLU98 3.8 19.6 1.0
O A:HOH1025 4.0 20.7 1.0
O A:HOH1034 4.0 24.1 1.0
O A:HOH1022 4.2 20.3 0.5
OE1 A:GLU98 4.2 20.9 1.0
O A:ASP146 4.4 33.2 1.0
N A:TYR148 4.5 18.9 1.0
CB A:ALA147 4.5 22.9 1.0
N A:ALA147 4.9 20.6 1.0

Manganese binding site 6 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 6 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn354

b:18.9
occ:0.30
 NE2 A:HIS86 2.4 20.1 1.0
OG A:SER82 2.4 25.4 1.0
O A:ARG83 2.6 28.7 1.0
CE1 A:HIS86 3.2 22.1 1.0
CD2 A:HIS86 3.5 22.4 1.0
CB A:SER82 3.6 22.7 1.0
OE1 A:GLN38 3.6 39.2 1.0
C A:ARG83 3.8 24.7 1.0
O A:HOH1040 4.0 24.9 1.0
C A:SER82 4.1 22.8 1.0
O A:ILE79 4.2 18.9 1.0
O A:SER82 4.2 23.1 1.0
N A:ARG83 4.3 25.4 1.0
ND1 A:HIS86 4.4 19.2 1.0
CA A:SER82 4.5 20.9 1.0
CG A:HIS86 4.5 19.0 1.0
CA A:GLY84 4.6 20.6 1.0
N A:GLY84 4.6 22.7 1.0
CA A:ARG83 4.7 25.7 1.0
C A:GLY84 4.8 19.9 1.0
CD A:GLN38 4.9 36.5 1.0
O A:GLY84 4.9 22.4 1.0
CG2 A:ILE79 4.9 25.0 1.0

Manganese binding site 7 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 7 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn355

b:37.4
occ:0.40
 ND2 A:ASN131 3.1 25.0 1.0
CE2 A:TYR123 3.8 22.8 0.8
OD1 A:ASN131 3.8 28.8 1.0
CG A:ASN131 3.9 23.4 1.0
CD A:LYS127 3.9 30.8 0.5
CD2 A:TYR123 4.0 28.3 0.8
CG A:PRO19 4.3 19.5 1.0
CB A:LYS127 4.4 25.1 1.0
CB A:PRO19 4.6 18.2 1.0
CG A:LYS127 4.6 26.8 0.5
CE A:LYS127 4.8 32.9 0.5
BR A:BR405 4.9 30.5 0.2
O A:HOH1106 4.9 37.9 1.0
O A:LYS127 4.9 21.4 1.0

Manganese binding site 8 out of 8 in 1y63

Go back to Manganese Binding Sites List in 1y63
Manganese binding site 8 out of 8 in the Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Initial Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn356

b:39.8
occ:0.35
 OH A:TYR90 2.7 25.8 1.0
CE1 A:HIS91 3.3 26.6 1.0
CD1 A:ILE64 3.4 44.8 1.0
CZ A:TYR90 3.6 22.4 1.0
CE1 A:TYR90 3.6 19.5 1.0
NE2 A:HIS91 4.0 36.6 1.0
CG1 A:VAL46 4.1 21.4 1.0
O A:THR61 4.3 52.1 0.7
ND1 A:HIS91 4.4 33.9 1.0
CG2 A:VAL46 4.5 21.6 1.0
CB A:VAL46 4.5 20.9 1.0
CG1 A:ILE64 4.7 40.6 1.0
O A:HOH1128 4.8 41.5 1.0
CE2 A:TYR90 4.9 21.2 1.0
CD1 A:TYR90 4.9 20.3 1.0
O A:HOH1051 5.0 26.9 1.0

Reference:

M.A.Robien, W.G.J.Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp). Crystal Structural Analysis of A Probable Kinase From Leishmania Major Friedlin To Be Published.
Page generated: Sat Oct 5 13:10:19 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