Calcium in PDB 1kze: Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide

The structure of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide, PDB code: 1kze was solved by K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.740, 75.220, 57.420, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.3

The structure of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide (pdb code 1kze). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide, PDB code: 1kze:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca501 b:12.7 occ:1.00 O 1:HOH1047 2.3 11.1 1.0 OD1 1:ASN199 2.4 15.6 1.0 OD1 1:ASP166 2.4 14.7 1.0 OD1 1:ASN193 2.5 15.0 1.0 O 1:GLU198 2.5 12.9 1.0 OE1 1:GLU170 2.5 13.6 1.0 OE2 1:GLU170 2.6 13.5 1.0 OD2 1:ASP166 2.7 13.8 1.0 CD 1:GLU170 2.9 13.6 1.0 CG 1:ASP166 2.9 13.9 1.0 CG 1:ASN193 3.3 18.5 1.0 C 1:GLU198 3.4 12.9 1.0 CG 1:ASN199 3.5 13.1 1.0 CA 1:ASN199 3.8 11.6 1.0 CB 1:ASN193 4.0 18.1 1.0 N 1:ASN199 4.0 12.2 1.0 CB 1:ASN199 4.1 12.0 1.0 ND2 1:ASN193 4.2 17.9 1.0 N 1:GLU198 4.3 16.2 1.0 CG 1:GLU170 4.4 15.5 1.0 O 1:HOH1046 4.4 19.4 1.0 CB 1:ASP166 4.4 12.9 1.0 CA 1:GLU198 4.5 14.2 1.0 ND2 1:ASN199 4.6 15.6 1.0 CA 1:ASN193 4.7 19.6 1.0 CZ 1:PHE173 4.7 17.2 1.0 OD1 1:ASP211 4.7 12.5 1.0 N 1:ASN171 4.8 14.6 1.0 O 1:ASP166 4.8 13.0 1.0 CA 1:GLU170 5.0 14.0 1.0 C 1:ASN199 5.0 10.3 1.0

Calcium binding site 2 out of 4 in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca502 b:13.2 occ:1.00 OD2 1:ASP211 2.3 11.8 1.0 OE2 1:GLU198 2.3 9.5 1.0 OD1 1:ASN192 2.4 16.1 1.0 OE2 1:GLU190 2.4 17.2 1.0 OD1 1:ASN210 2.5 13.9 1.0 O3 1:MAN1001 2.5 19.8 1.0 O 1:ASP211 2.6 11.6 1.0 O4 1:MAN1001 2.6 15.4 1.0 CG 1:ASP211 3.3 13.3 1.0 CD 1:GLU198 3.3 9.2 1.0 C3 1:MAN1001 3.4 19.3 1.0 CD 1:GLU190 3.4 17.3 1.0 CG 1:ASN192 3.4 18.1 1.0 C4 1:MAN1001 3.4 18.1 1.0 CG 1:ASN210 3.5 16.1 1.0 C 1:ASP211 3.6 10.5 1.0 OE1 1:GLU198 3.6 11.4 1.0 OE1 1:GLU190 3.7 19.8 1.0 N 1:ASP211 3.7 10.2 1.0 ND2 1:ASN192 3.8 19.2 1.0 ND2 1:ASN210 3.9 12.1 1.0 OD1 1:ASP211 3.9 12.5 1.0 CA 1:ASP211 4.1 10.4 1.0 N 1:ASN192 4.2 17.8 1.0 CB 1:ASP211 4.2 10.3 1.0 CG2 1:VAL194 4.5 27.1 1.0 CG 1:GLU198 4.6 11.8 1.0 N 1:ASN193 4.6 17.4 1.0 CB 1:ASN192 4.6 18.1 1.0 C 1:ASN210 4.6 10.7 1.0 CG 1:GLU190 4.6 15.4 1.0 CB 1:GLU198 4.8 12.5 1.0 N 1:VAL212 4.8 9.7 1.0 CA 1:ASN192 4.8 18.1 1.0 CB 1:ASN210 4.8 11.4 1.0 C2 1:MAN1001 4.8 19.1 1.0 C5 1:MAN1001 4.8 21.4 1.0 CG1 1:VAL194 4.8 28.2 1.0 CA 1:ASN210 4.9 12.1 1.0 N 1:VAL194 4.9 23.0 1.0 C 1:ASN192 5.0 19.5 1.0

Calcium binding site 3 out of 4 in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca601 b:14.6 occ:1.00 OD1 2:ASN199 2.3 15.8 1.0 O 2:HOH2006 2.3 13.8 1.0 OD2 2:ASP166 2.4 14.9 1.0 OE2 2:GLU170 2.5 15.8 1.0 OE1 2:GLU170 2.5 18.0 1.0 O 2:GLU198 2.5 10.8 1.0 OD1 2:ASN193 2.5 16.5 1.0 OD1 2:ASP166 2.7 14.7 1.0 CD 2:GLU170 2.8 14.8 1.0 CG 2:ASP166 2.9 15.0 1.0 CG 2:ASN193 3.3 20.6 1.0 CG 2:ASN199 3.4 14.5 1.0 C 2:GLU198 3.4 13.5 1.0 CA 2:ASN199 3.8 12.8 1.0 N 2:ASN199 4.0 11.7 1.0 CB 2:ASN193 4.0 17.7 1.0 CB 2:ASN199 4.1 14.1 1.0 O 2:HOH2009 4.2 16.8 1.0 ND2 2:ASN193 4.2 20.9 1.0 CG 2:GLU170 4.3 17.9 1.0 N 2:GLU198 4.4 17.2 1.0 O 2:HOH2005 4.4 17.8 1.0 O 2:HOH2007 4.4 37.5 1.0 CB 2:ASP166 4.4 14.5 1.0 ND2 2:ASN199 4.5 20.0 1.0 CA 2:GLU198 4.5 13.2 1.0 CA 2:ASN193 4.7 19.1 1.0 OD1 2:ASP211 4.7 12.9 1.0 N 2:ASN171 4.8 17.4 1.0 CZ 2:PHE173 4.8 17.9 1.0 O 2:ASP166 4.8 18.5 1.0 CA 2:GLU170 4.9 18.0 1.0 CB 2:GLU170 5.0 18.5 1.0 C 2:ASN199 5.0 11.5 1.0

Calcium binding site 4 out of 4 in the Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Mbp-C and Bivalent Man-Terminated Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca602 b:13.0 occ:1.00 OE2 2:GLU198 2.3 13.3 1.0 OD2 2:ASP211 2.4 11.1 1.0 OD1 2:ASN192 2.4 14.3 1.0 OD1 2:ASN210 2.5 13.2 1.0 O3 2:MAN2001 2.5 15.1 1.0 O 2:ASP211 2.5 11.5 1.0 OE2 2:GLU190 2.6 12.8 1.0 O4 2:MAN2001 2.6 16.3 1.0 CG 2:ASP211 3.3 12.0 1.0 CD 2:GLU198 3.3 12.1 1.0 C3 2:MAN2001 3.4 17.8 1.0 CG 2:ASN192 3.4 17.0 1.0 C4 2:MAN2001 3.5 17.2 1.0 CD 2:GLU190 3.5 12.8 1.0 CG 2:ASN210 3.5 14.6 1.0 C 2:ASP211 3.6 11.5 1.0 OE1 2:GLU198 3.6 14.3 1.0 OE1 2:GLU190 3.7 11.7 1.0 N 2:ASP211 3.8 9.0 1.0 ND2 2:ASN192 3.9 15.4 1.0 OD1 2:ASP211 3.9 12.9 1.0 ND2 2:ASN210 4.0 14.4 1.0 CA 2:ASP211 4.1 11.2 1.0 N 2:ASN192 4.2 17.4 1.0 CB 2:ASP211 4.3 9.6 1.0 CG1 2:VAL194 4.3 25.0 1.0 CG 2:GLU198 4.6 13.6 1.0 N 2:ASN193 4.6 18.0 1.0 C 2:ASN210 4.7 10.7 1.0 CB 2:ASN192 4.7 16.8 1.0 CG 2:GLU190 4.7 13.5 1.0 CB 2:GLU198 4.8 14.5 1.0 N 2:VAL212 4.8 11.2 1.0 C2 2:MAN2001 4.8 17.2 1.0 CB 2:ASN210 4.8 11.8 1.0 CA 2:ASN192 4.8 18.1 1.0 C5 2:MAN2001 4.9 20.0 1.0 N 2:VAL194 4.9 20.3 1.0 CA 2:ASN210 5.0 11.2 1.0

K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis. Orientation of Bound Ligands in Mannose-Binding Proteins. Implications For Multivalent Ligand Recognition. J.Biol.Chem. V. 277 16088 2002.
ISSN: ISSN 0021-9258
PubMed: 11850428
DOI: 10.1074/JBC.M200493200