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Manganese in PDB 4k28: 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+

Protein crystallography data

The structure of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+, PDB code: 4k28 was solved by C.Garcia, J.Peek, P.Petit, D.Christendat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.22 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.437, 76.688, 153.333, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.8

Other elements in 4k28:

The structure of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ (pdb code 4k28). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+, PDB code: 4k28:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4k28

Go back to Manganese Binding Sites List in 4k28
Manganese binding site 1 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:69.3
occ:0.72
 CB A:CYS155 2.5 10.6 1.0
SG A:CYS155 2.6 60.3 1.0
O A:HOH484 3.3 43.5 1.0
CZ A:PHE182 3.4 25.7 1.0
CD2 A:LEU207 3.5 33.9 1.0
CE1 A:PHE182 4.0 24.6 1.0
CA A:CYS155 4.1 20.5 1.0
CG1 A:ILE131 4.2 15.8 1.0
CE2 A:PHE182 4.5 24.3 1.0
CD1 A:LEU129 4.6 10.8 1.0
CG2 A:ILE131 4.6 16.7 1.0
O A:HOH462 4.7 35.5 1.0
CD2 A:LEU129 4.7 15.0 1.0
N A:CYS155 4.8 16.1 1.0
CD1 A:ILE131 4.8 18.2 1.0
CB A:ILE131 4.9 13.7 1.0
C A:CYS155 4.9 17.9 1.0
CG A:LEU207 4.9 32.8 1.0

Manganese binding site 2 out of 6 in 4k28

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Manganese binding site 2 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:38.8
occ:0.67
 SG A:CYS166 2.2 29.7 1.0
CG1 A:VAL178 2.9 31.4 1.0
CB A:CYS166 3.0 15.5 1.0
CB A:VAL178 3.6 26.9 1.0
CA A:CYS166 3.6 13.3 1.0
CG2 A:THR180 3.8 20.9 1.0
N A:SER179 4.0 19.8 1.0
C A:VAL178 4.1 23.1 1.0
CD1 A:LEU154 4.2 14.5 1.0
CA A:SER179 4.3 20.1 1.0
C A:SER179 4.3 17.9 1.0
O A:VAL178 4.4 25.2 1.0
O A:SER179 4.5 15.2 1.0
CA A:VAL178 4.5 22.4 1.0
N A:CYS166 4.6 11.6 1.0
C A:CYS166 4.7 16.6 1.0
CG2 A:VAL178 4.8 25.0 1.0
N A:THR180 4.8 16.4 1.0
O A:CYS166 4.8 14.9 1.0

Manganese binding site 3 out of 6 in 4k28

Go back to Manganese Binding Sites List in 4k28
Manganese binding site 3 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:75.3
occ:0.69
 SG A:CYS34 2.4 43.0 1.0
CB A:CYS34 3.1 47.7 1.0
CA A:CYS34 3.7 47.6 1.0
CD1 A:LEU36 4.4 41.8 1.0
N A:CYS34 4.6 49.1 1.0
O A:ASN32 4.8 44.5 1.0
C A:CYS34 4.9 44.0 1.0
CZ3 A:TRP28 5.0 41.3 1.0

Manganese binding site 4 out of 6 in 4k28

Go back to Manganese Binding Sites List in 4k28
Manganese binding site 4 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:56.1
occ:0.69
 SG B:CYS34 2.4 45.6 1.0
CB B:CYS34 3.3 48.2 1.0
CA B:CYS34 3.5 46.9 1.0
N B:CYS34 3.6 48.8 1.0
C B:ASN33 4.3 54.0 1.0
N B:ASN33 4.4 47.1 1.0
CB B:ASN32 4.6 40.8 1.0
CZ3 B:TRP28 4.8 40.4 1.0
C B:CYS34 4.9 45.4 1.0
CA B:ASN33 4.9 53.1 1.0
O B:ASN33 4.9 57.6 1.0
CH2 B:TRP28 4.9 39.7 1.0

Manganese binding site 5 out of 6 in 4k28

Go back to Manganese Binding Sites List in 4k28
Manganese binding site 5 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:70.8
occ:0.75
 SG B:CYS155 2.3 77.2 1.0
CB B:CYS155 2.5 17.4 1.0
CD2 B:LEU207 3.5 28.8 1.0
CZ B:PHE182 3.7 25.4 1.0
CA B:CYS155 4.0 18.2 1.0
CE1 B:PHE182 4.2 23.5 1.0
CG1 B:ILE131 4.3 17.7 1.0
CG2 B:ILE131 4.6 18.4 1.0
CD1 B:LEU129 4.6 10.2 1.0
CD1 B:ILE131 4.7 21.7 1.0
CE2 B:PHE182 4.8 23.2 1.0
C B:CYS155 4.8 22.5 1.0
CD2 B:LEU129 4.8 7.8 1.0
N B:CYS155 4.8 16.9 1.0
CG B:LEU207 5.0 29.0 1.0
CB B:ILE131 5.0 17.9 1.0
CD1 B:LEU211 5.0 25.0 1.0

Manganese binding site 6 out of 6 in 4k28

Go back to Manganese Binding Sites List in 4k28
Manganese binding site 6 out of 6 in the 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2.15 Angstrom Resolution Crystal Structure of A Shikimate Dehydrogenase Family Protein From Pseudomonas Putida KT2440 in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn305

b:55.6
occ:0.65
 SG B:CYS166 2.5 46.9 1.0
CG1 B:VAL178 2.8 30.2 1.0
CB B:CYS166 3.3 29.6 1.0
CB B:VAL178 3.5 27.6 1.0
C B:VAL178 3.9 24.7 1.0
CA B:CYS166 4.0 27.1 1.0
O B:VAL178 4.0 23.3 1.0
N B:SER179 4.0 24.6 1.0
CG2 B:THR180 4.1 17.2 1.0
CA B:VAL178 4.3 22.5 1.0
CA B:SER179 4.4 24.1 1.0
C B:SER179 4.5 24.0 1.0
CD1 B:LEU154 4.5 17.9 1.0
CG2 B:VAL178 4.7 25.7 1.0
O B:SER179 4.7 27.3 1.0
N B:THR180 4.9 23.3 1.0
C B:CYS166 4.9 29.5 1.0
N B:CYS166 5.0 21.6 1.0

Reference:

J.Peek, C.Garcia, J.Lee, D.Christendat. Insights Into the Function of RIFI2: Structural and Biochemical Investigation of A New Shikimate Dehydrogenase Family Protein. Biochim.Biophys.Acta V.1834 516 2013.
ISSN: ISSN 0006-3002
PubMed: 23142411
DOI: 10.1016/J.BBAPAP.2012.10.016
Page generated: Sat Oct 5 20:00:25 2024

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