Nickel in PDB 7wcy: Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope

The structure of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope, PDB code: 7wcy was solved by Y.L.Wang, M.H.Gao, L.X.Zhang, S.H.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.92, 84.77, 95.24, 90, 90, 90
R / Rfree (%)	22.6 / 25.8

The binding sites of Nickel atom in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope (pdb code 7wcy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope, PDB code: 7wcy:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:105.9 occ:0.92 NE2 A:HIS191 2.3 72.6 1.0 O A:GLU275 2.3 51.8 1.0 C A:GLU275 2.7 68.9 1.0 CD2 A:HIS191 2.9 86.0 1.0 CE1 A:HIS191 3.0 76.4 1.0 CG A:HIS191 3.8 84.5 1.0 ND1 A:HIS191 3.8 81.1 1.0 CA A:GLU275 4.1 86.8 1.0 N A:GLU275 4.3 103.6 1.0 CG A:GLU275 4.8 90.9 1.0 O A:VAL189 4.8 83.2 1.0 N A:HIS191 4.9 74.7 1.0

Nickel binding site 2 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni601 b:80.2 occ:1.00 O B:HOH701 2.0 51.6 1.0 CE1 B:HIS67 3.2 101.8 1.0 ND1 B:HIS67 3.7 85.5 1.0 NE2 B:HIS67 4.1 102.6 1.0 OE2 B:GLU69 4.3 103.0 1.0 CG B:HIS67 4.8 85.8 1.0 O B:HOH706 4.9 55.3 1.0

Nickel binding site 3 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni602 b:85.0 occ:1.00 OE2 B:GLU36 1.9 48.0 1.0 CD B:GLU36 2.8 90.1 1.0 CE1 B:HIS34 2.9 85.3 1.0 CG B:GLU36 3.2 89.0 1.0 NE2 B:HIS34 3.6 90.7 1.0 ND1 B:HIS34 3.9 77.2 1.0 OE1 B:GLU36 3.9 93.7 1.0 CB B:GLU36 4.7 85.9 1.0 CD2 B:HIS34 4.8 91.0 1.0 CG B:HIS34 5.0 86.4 1.0

Nickel binding site 4 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni601 b:79.5 occ:1.00 O D:HOH715 1.7 66.0 1.0 NE2 D:HIS260 2.1 55.8 1.0 NE2 A:HIS145 2.5 61.5 1.0 O A:HOH401 2.5 47.7 1.0 CE1 D:HIS260 2.7 72.9 1.0 CD2 A:HIS145 3.1 66.6 1.0 CD2 D:HIS260 3.3 60.7 1.0 NE2 D:GLN218 3.5 99.8 1.0 CE1 A:HIS145 3.7 72.1 1.0 ND1 D:HIS260 3.9 76.3 1.0 CG A:GLN149 4.2 69.4 1.0 CG D:HIS260 4.2 59.6 1.0 OE1 A:GLN149 4.3 89.9 1.0 CD A:GLN149 4.4 81.1 1.0 CG A:HIS145 4.4 70.2 1.0 CD D:GLN218 4.6 90.2 1.0 ND1 A:HIS145 4.6 66.1 1.0

Nickel binding site 5 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni602 b:74.2 occ:1.00 O D:HOH709 1.6 70.7 1.0 NE2 D:HIS145 2.1 60.8 1.0 CD2 D:HIS145 3.0 55.7 1.0 CE1 D:HIS145 3.2 64.4 1.0 OE1 D:GLN149 4.0 118.2 1.0 CG D:GLN149 4.1 92.5 1.0 CD D:GLN149 4.1 103.8 1.0 CG D:HIS145 4.2 66.6 1.0 ND1 D:HIS145 4.2 61.8 1.0 NE2 D:GLN149 4.9 101.5 1.0

Nickel binding site 6 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni603 b:89.0 occ:1.00 NE2 D:HIS191 1.6 81.1 1.0 CE1 D:HIS191 2.2 79.6 1.0 C D:GLU275 2.9 81.4 1.0 CD2 D:HIS191 2.9 84.7 1.0 O D:GLU275 3.2 68.9 1.0 ND1 D:HIS191 3.5 87.8 1.0 CG D:HIS191 3.8 85.5 1.0 CA D:GLU275 4.1 82.1 1.0 CB D:GLU275 4.4 86.4 1.0 N D:GLU275 4.7 81.8 1.0 CG D:GLU275 4.9 93.3 1.0

Nickel binding site 7 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni601 b:92.1 occ:1.00 NE2 E:HIS67 2.7 95.7 1.0 CD2 E:HIS67 3.2 84.2 1.0 OE2 E:GLU69 3.5 77.7 1.0 CE1 E:HIS67 3.8 94.2 1.0 CG E:HIS67 4.4 83.1 1.0 CD E:GLU69 4.6 90.3 1.0 ND1 E:HIS67 4.7 93.7 1.0 OE1 E:GLU69 4.8 98.5 1.0

Nickel binding site 8 out of 8 in the Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of H-2KB with Cryptosporidium Parvum GP40/15 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni602 b:89.4 occ:1.00 OE2 E:GLU36 1.9 93.3 1.0 NE2 E:HIS34 2.5 76.3 1.0 CD E:GLU36 2.6 97.4 1.0 CG E:GLU36 3.0 92.7 1.0 CE1 E:HIS34 3.2 77.5 1.0 CD2 E:HIS34 3.6 70.1 1.0 OE1 E:GLU36 3.7 97.8 1.0 ND1 E:HIS34 4.3 71.6 1.0 CB E:GLU36 4.5 79.7 1.0 CG E:HIS34 4.6 69.6 1.0

Y.L.Wang, M.H.Gao, W.S.Zhu, L.X.Zhang, S.H.Fan. Structural Analyses of A Dominant Cryptosporidium Parvum Epitope Presented By H-2KB Offer New Options to Combat Cryptosporidiosis Mbio 2022.
ISSN: ESSN 2150-7511