Manganese in PDB 4lfi: Crystal Structure of SCCK2 Alpha in Complex with Gmppnp

All present enzymatic activity of Crystal Structure of SCCK2 Alpha in Complex with Gmppnp:
2.7.11.1;

The structure of Crystal Structure of SCCK2 Alpha in Complex with Gmppnp, PDB code: 4lfi was solved by H.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.86 / 1.85
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	69.664, 69.664, 166.251, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20

The binding sites of Manganese atom in the Crystal Structure of SCCK2 Alpha in Complex with Gmppnp (pdb code 4lfi). 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 SCCK2 Alpha in Complex with Gmppnp, PDB code: 4lfi:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of SCCK2 Alpha in Complex with Gmppnp


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 SCCK2 Alpha in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:21.7 occ:1.00 O2A A:GNP401 2.0 20.9 1.0 OD1 A:ASN200 2.1 20.9 1.0 O A:HOH506 2.2 22.3 1.0 OD2 A:ASP214 2.2 19.8 1.0 O3G A:GNP401 2.2 23.1 1.0 N3B A:GNP401 2.6 22.0 1.0 PG A:GNP401 2.9 24.2 1.0 CG A:ASP214 3.1 18.7 1.0 CG A:ASN200 3.1 20.7 1.0 PA A:GNP401 3.3 21.0 1.0 ND2 A:ASN200 3.5 21.9 1.0 CB A:ASP214 3.6 18.9 1.0 PB A:GNP401 3.6 22.6 1.0 O1G A:GNP401 3.7 23.8 1.0 O3A A:GNP401 3.8 21.6 1.0 MN A:MN403 3.9 24.1 1.0 O1B A:GNP401 4.0 22.9 1.0 CE A:LYS197 4.1 25.0 1.0 OD1 A:ASP214 4.1 19.9 1.0 O2G A:GNP401 4.3 24.6 1.0 O3' A:GNP401 4.3 22.5 1.0 O5' A:GNP401 4.3 22.6 1.0 NZ A:LYS197 4.4 26.4 1.0 O A:HOH580 4.4 31.1 1.0 C5' A:GNP401 4.4 22.3 1.0 O1A A:GNP401 4.4 22.0 1.0 CB A:ASN200 4.5 20.7 1.0 O A:HIS199 4.5 22.1 1.0 OD2 A:ASP195 4.5 21.7 1.0 CA A:ASN200 4.8 19.6 1.0 C A:HIS199 4.8 20.8 1.0 O A:HOH539 4.9 23.7 1.0 C3' A:GNP401 4.9 22.3 1.0 N A:ASN200 4.9 20.3 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of SCCK2 Alpha in Complex with Gmppnp


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 SCCK2 Alpha in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:24.1 occ:1.00 O1G A:GNP401 2.1 23.8 1.0 O A:HOH539 2.1 23.7 1.0 O1B A:GNP401 2.2 22.9 1.0 O A:HOH551 2.2 22.4 1.0 OD1 A:ASP214 2.3 19.9 1.0 OD2 A:ASP214 2.3 19.8 1.0 CG A:ASP214 2.6 18.7 1.0 PG A:GNP401 3.2 24.2 1.0 PB A:GNP401 3.3 22.6 1.0 N3B A:GNP401 3.5 22.0 1.0 O3G A:GNP401 3.8 23.1 1.0 CD2 A:TYR51 3.9 27.6 1.0 MN A:MN402 3.9 21.7 1.0 OD2 A:ASP195 4.0 21.7 1.0 CB A:ASP214 4.1 18.9 1.0 O A:HOH535 4.2 23.6 1.0 O A:HOH624 4.2 30.2 1.0 NZ A:LYS69 4.3 22.5 1.0 O2B A:GNP401 4.4 23.4 1.0 O3A A:GNP401 4.4 21.6 1.0 O2G A:GNP401 4.6 24.6 1.0 CE2 A:TYR51 4.6 28.2 1.0 O2A A:GNP401 4.6 20.9 1.0 N A:GLY216 4.7 23.3 1.0 CA A:GLY216 4.7 23.1 1.0 CG A:TYR51 4.8 26.9 1.0 O A:HOH621 4.8 34.5 1.0 O A:ASP214 4.8 20.2 1.0 CB A:TYR51 4.8 25.4 1.0 CG A:LEU217 4.9 25.5 1.0 CA A:ASP214 4.9 19.5 1.0 PA A:GNP401 4.9 21.0 1.0 N A:LEU217 4.9 22.4 1.0 C A:GLY216 4.9 23.4 1.0 C A:ASP214 5.0 20.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of SCCK2 Alpha in Complex with Gmppnp


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 SCCK2 Alpha in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:24.0 occ:1.00 O3G B:GNP401 2.0 24.1 1.0 O2B B:GNP401 2.2 23.4 1.0 O B:HOH538 2.2 24.2 1.0 O B:HOH550 2.2 24.1 1.0 OD2 B:ASP214 2.2 19.4 1.0 OD1 B:ASP214 2.3 18.7 1.0 CG B:ASP214 2.6 17.7 1.0 PG B:GNP401 3.2 24.7 1.0 PB B:GNP401 3.3 23.2 1.0 N3B B:GNP401 3.5 22.7 1.0 O2G B:GNP401 3.9 23.4 1.0 CD2 B:TYR51 3.9 27.0 1.0 MN B:MN403 3.9 21.6 1.0 OD2 B:ASP195 4.0 22.0 1.0 CB B:ASP214 4.2 18.5 1.0 O B:HOH524 4.2 22.9 1.0 O B:HOH633 4.3 28.5 1.0 O1B B:GNP401 4.3 23.6 1.0 NZ B:LYS69 4.4 24.1 1.0 O1G B:GNP401 4.4 24.7 1.0 O3A B:GNP401 4.4 21.1 1.0 CE2 B:TYR51 4.5 28.3 1.0 O2A B:GNP401 4.6 20.7 1.0 CA B:GLY216 4.7 22.7 1.0 N B:GLY216 4.7 22.7 1.0 CG B:TYR51 4.7 27.2 1.0 O B:HOH589 4.8 32.8 1.0 CB B:TYR51 4.8 24.8 1.0 CG B:LEU217 4.9 24.4 1.0 PA B:GNP401 4.9 20.7 1.0 N B:LEU217 4.9 22.2 1.0 O B:ASP214 4.9 20.1 1.0 CA B:ASP214 4.9 19.2 1.0 C B:GLY216 5.0 22.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of SCCK2 Alpha in Complex with Gmppnp


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 SCCK2 Alpha in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:21.6 occ:1.00 O2A B:GNP401 2.0 20.7 1.0 O B:HOH503 2.1 21.8 1.0 OD1 B:ASN200 2.1 19.9 1.0 OD2 B:ASP214 2.2 19.4 1.0 O2G B:GNP401 2.2 23.4 1.0 N3B B:GNP401 2.5 22.7 1.0 PG B:GNP401 2.9 24.7 1.0 CG B:ASP214 3.1 17.7 1.0 CG B:ASN200 3.1 20.0 1.0 PA B:GNP401 3.3 20.7 1.0 ND2 B:ASN200 3.5 21.2 1.0 CB B:ASP214 3.6 18.5 1.0 PB B:GNP401 3.6 23.2 1.0 O3G B:GNP401 3.7 24.1 1.0 O3A B:GNP401 3.8 21.1 1.0 MN B:MN402 3.9 24.0 1.0 O2B B:GNP401 4.0 23.4 1.0 OD1 B:ASP214 4.1 18.7 1.0 O1G B:GNP401 4.1 24.7 1.0 CE B:LYS197 4.2 24.2 1.0 O3' B:GNP401 4.3 22.1 1.0 O5' B:GNP401 4.3 21.5 1.0 C5' B:GNP401 4.4 21.2 1.0 O B:HOH584 4.4 32.1 1.0 O1A B:GNP401 4.4 21.4 1.0 NZ B:LYS197 4.4 24.7 1.0 CB B:ASN200 4.5 20.3 1.0 O B:HIS199 4.5 21.0 1.0 OD2 B:ASP195 4.5 22.0 1.0 CA B:ASN200 4.8 19.4 1.0 C B:HIS199 4.8 20.9 1.0 C3' B:GNP401 4.9 21.6 1.0 O B:HOH550 4.9 24.1 1.0 O1B B:GNP401 4.9 23.6 1.0 N B:ASN200 5.0 19.9 1.0

H.Liu, H.Wang, M.Teng, X.Li. The Multiple Nucleotide-Divalent Cation Binding Modes of Saccharomyces Cerevisiae CK2 Alpha Indicate A Possible Co-Substrate Hydrolysis Product (Adp/Gdp) Release Pathway. Acta Crystallogr.,Sect.D V. 70 501 2014.
ISSN: ISSN 0907-4449
PubMed: 24531484
DOI: 10.1107/S1399004713027879