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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

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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

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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

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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

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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

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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

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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

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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

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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

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