Manganese in PDB 4kqb: Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound

The structure of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound, PDB code: 4kqb was solved by J.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 3.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.490, 101.702, 158.765, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.3

The structure of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound (pdb code 4kqb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound, PDB code: 4kqb:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn606 b:90.0 occ:1.00 OE1 A:GLU213 2.1 61.3 1.0 O3B A:ADP608 2.4 70.5 1.0 OD1 A:ASP387 2.5 58.0 1.0 CD A:GLU213 3.1 59.0 1.0 OD2 A:ASP387 3.1 61.8 1.0 CG A:ASP387 3.1 59.2 1.0 OD2 A:ASP366 3.5 48.5 1.0 CG A:GLU213 3.7 56.0 1.0 PB A:ADP608 3.8 70.7 1.0 OE2 A:GLU213 4.0 58.7 1.0 MN A:MN607 4.2 68.5 1.0 CD A:ARG390 4.2 50.2 1.0 O2B A:ADP608 4.4 69.6 1.0 O1B A:ADP608 4.4 71.9 1.0 NE2 A:GLN176 4.6 66.6 1.0 CB A:ASP387 4.6 55.1 1.0 CG A:ARG390 4.6 47.4 1.0 NE A:ARG390 4.6 53.3 1.0 CG A:ASP366 4.6 46.5 1.0 NH1 A:ARG390 4.8 57.2 1.0 O1A A:ADP608 4.8 65.4 1.0 N A:ARG390 4.8 42.4 1.0 O3A A:ADP608 4.9 0.3 1.0 CZ A:ARG390 4.9 56.3 1.0 N A:GLY389 4.9 48.4 1.0 NZ A:LYS192 4.9 36.4 1.0 CB A:ARG390 5.0 45.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn607 b:68.5 occ:1.00 O1A A:ADP608 2.0 65.4 1.0 OD2 A:ASP387 2.0 61.8 1.0 O1B A:ADP608 2.7 71.9 1.0 O3B A:ADP608 3.1 70.5 1.0 CG A:ASP387 3.2 59.2 1.0 PB A:ADP608 3.4 70.7 1.0 PA A:ADP608 3.4 65.9 1.0 O3A A:ADP608 3.9 0.3 1.0 OD1 A:ASP387 4.0 58.0 1.0 NE2 A:HIS368 4.1 59.2 1.0 CB A:ASP387 4.1 55.1 1.0 C5' A:ADP608 4.2 70.8 1.0 MN A:MN606 4.2 90.0 1.0 O5' A:ADP608 4.3 70.8 1.0 CE1 A:HIS368 4.4 58.2 1.0 O2A A:ADP608 4.4 65.0 1.0 O2B A:ADP608 4.8 69.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn606 b:76.6 occ:1.00 OE1 B:GLU213 2.1 56.2 1.0 OD1 B:ASP387 2.5 55.1 1.0 O1B B:ADP608 3.1 58.5 1.0 CD B:GLU213 3.2 57.4 1.0 CG B:ASP387 3.2 55.6 1.0 OD2 B:ASP387 3.2 56.2 1.0 OD2 B:ASP366 3.3 59.5 1.0 O3B B:ADP608 3.5 60.7 1.0 PB B:ADP608 3.8 60.8 1.0 CG B:GLU213 3.8 54.2 1.0 CD B:ARG390 4.1 47.7 1.0 OE2 B:GLU213 4.1 59.9 1.0 MN B:MN607 4.3 79.7 1.0 CG B:ASP366 4.4 59.2 1.0 NH1 B:ARG390 4.4 56.1 1.0 NE B:ARG390 4.5 49.9 1.0 CG B:ARG390 4.6 46.0 1.0 O2B B:ADP608 4.6 63.5 1.0 CB B:ASP387 4.6 55.8 1.0 CZ B:ARG390 4.7 54.2 1.0 NE2 B:GLN176 4.9 66.1 1.0 CB B:ARG390 4.9 45.0 1.0 CB B:ASP366 4.9 57.1 1.0 N B:ARG390 5.0 50.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Golgi Casein Kinase with Mn/Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn607 b:79.7 occ:1.00 OD2 B:ASP387 2.1 56.2 1.0 O1B B:ADP608 2.1 58.5 1.0 O1A B:ADP608 2.3 53.4 1.0 CG B:ASP387 3.2 55.6 1.0 PB B:ADP608 3.4 60.8 1.0 PA B:ADP608 3.5 50.8 1.0 O3A B:ADP608 3.5 0.0 1.0 OD1 B:ASP387 4.0 55.1 1.0 CB B:ASP387 4.1 55.8 1.0 CE1 B:HIS368 4.2 75.5 1.0 MN B:MN606 4.3 76.6 1.0 O2B B:ADP608 4.4 63.5 1.0 O3B B:ADP608 4.4 60.7 1.0 C5' B:ADP608 4.4 70.1 1.0 O5' B:ADP608 4.4 68.8 1.0 NE2 B:HIS368 4.6 75.3 1.0 O2A B:ADP608 4.6 47.4 1.0 CA B:GLY174 4.8 56.3 1.0

J.Xiao, V.S.Tagliabracci, J.Wen, S.A.Kim, J.E.Dixon. Crystal Structure of the Golgi Casein Kinase. Proc.Natl.Acad.Sci.Usa V. 110 10574 2013.
ISSN: ISSN 0027-8424
PubMed: 23754375
DOI: 10.1073/PNAS.1309211110