Calcium in PDB 6kzb: TRANSGLUTAMINASE2 Complexed with Calcium

All present enzymatic activity of TRANSGLUTAMINASE2 Complexed with Calcium:
2.3.2.13;

The structure of TRANSGLUTAMINASE2 Complexed with Calcium, PDB code: 6kzb was solved by H.H.Park, C.M.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.59 / 3.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	133.080, 216.307, 166.263, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.2

The binding sites of Calcium atom in the TRANSGLUTAMINASE2 Complexed with Calcium (pdb code 6kzb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the TRANSGLUTAMINASE2 Complexed with Calcium, PDB code: 6kzb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:70.3 occ:1.00 ND2 A:ASN498 3.1 62.4 1.0 OE2 A:GLU539 4.0 56.7 1.0 O A:PHE537 4.2 63.6 1.0 CG A:ASN498 4.3 73.2 1.0 CG A:GLU539 4.4 55.9 1.0 C A:PHE537 4.5 60.7 1.0 O A:ASN497 4.5 65.2 1.0 CD A:GLU539 4.7 55.6 1.0 N A:SER538 4.7 61.5 1.0 CG2 A:THR496 4.7 67.7 1.0 CA A:SER538 4.9 54.3 1.0 CB A:ASN498 4.9 74.4 1.0

Calcium binding site 2 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:70.4 occ:1.00 NH1 A:ARG296 3.2 52.8 1.0 OE2 A:GLU437 3.4 56.0 1.0 OE1 A:GLU437 3.6 58.1 1.0 OH A:TYR159 3.7 47.4 1.0 CD A:GLU437 3.9 55.3 1.0 CZ A:ARG296 4.3 50.7 1.0 NE1 A:TRP354 4.6 50.2 1.0 NH2 A:ARG296 4.7 47.5 1.0 OE1 A:GLU155 4.7 72.2 1.0 CZ A:TYR159 4.8 48.8 1.0 CE2 A:TYR159 5.0 49.8 1.0

Calcium binding site 3 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:75.2 occ:1.00 OD1 B:ASN498 3.2 68.8 1.0 OE2 B:GLU539 3.9 77.0 1.0 O C:SER541 4.0 49.9 1.0 CG B:GLU539 4.0 73.8 1.0 N C:SER541 4.1 64.5 1.0 NZ C:LYS540 4.1 81.3 1.0 CD B:GLU539 4.2 74.0 1.0 O B:PHE537 4.2 76.3 1.0 CG B:ASN498 4.4 72.4 1.0 CD C:LYS540 4.4 68.6 1.0 C B:PHE537 4.4 73.2 1.0 CB C:SER541 4.5 60.9 1.0 CG2 B:THR496 4.6 67.0 1.0 N B:SER538 4.6 69.4 1.0 CA B:SER538 4.7 73.0 1.0 CA C:SER541 4.7 59.2 1.0 CE C:LYS540 4.7 75.6 1.0 C B:SER538 4.8 75.5 1.0 C C:SER541 4.8 56.3 1.0 N B:GLU539 5.0 77.6 1.0

Calcium binding site 4 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:47.0 occ:1.00 NH1 B:ARG296 3.1 53.2 1.0 OH B:TYR159 3.7 37.5 1.0 OE2 B:GLU437 3.9 36.0 1.0 NE1 B:TRP354 3.9 55.5 1.0 CZ B:ARG296 4.2 48.4 1.0 OE1 B:GLU155 4.3 60.2 1.0 NH2 B:ARG296 4.4 45.3 1.0 OE1 B:GLU437 4.5 52.1 1.0 CD B:GLU155 4.6 48.1 1.0 CE2 B:TYR159 4.6 51.5 1.0 CZ B:TYR159 4.6 48.0 1.0 CD B:GLU437 4.7 52.9 1.0 OE2 B:GLU155 4.7 46.0 1.0 CZ2 B:TRP354 4.7 46.4 1.0 CE2 B:TRP354 4.7 46.2 1.0 CD1 B:TRP354 5.0 54.4 1.0

Calcium binding site 5 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:90.3 occ:1.00 O C:PHE537 3.8 70.6 1.0 OD1 C:ASN498 3.9 91.2 1.0 C C:PHE537 4.0 68.6 1.0 O C:ASN497 4.1 90.3 1.0 N C:SER538 4.3 66.4 1.0 CD B:LYS540 4.5 65.4 1.0 CA C:PHE537 4.5 76.8 1.0 CG2 C:THR496 4.6 84.1 1.0 CA C:SER538 4.6 67.0 1.0 CG C:ASN498 4.6 0.3 1.0 O B:SER541 4.6 78.0 1.0 CG C:GLU539 4.7 72.0 1.0 CA C:ASN498 4.7 94.1 1.0 CB C:ASN498 4.8 96.5 1.0 C C:SER538 4.8 68.0 1.0 C C:ASN497 4.9 89.6 1.0 OE2 C:GLU539 5.0 82.1 1.0 OG B:SER541 5.0 67.7 1.0

Calcium binding site 6 out of 6 in the TRANSGLUTAMINASE2 Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of TRANSGLUTAMINASE2 Complexed with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:62.5 occ:1.00 NH1 C:ARG296 3.3 54.9 1.0 OE2 C:GLU437 3.6 70.1 1.0 NE1 C:TRP354 4.1 55.2 1.0 OH C:TYR159 4.1 52.4 1.0 OE1 C:GLU437 4.3 68.1 1.0 CZ C:ARG296 4.3 53.9 1.0 OE1 C:GLU155 4.3 79.0 1.0 CD C:GLU437 4.4 71.3 1.0 NH2 C:ARG296 4.5 54.9 1.0 CE2 C:TRP354 4.9 52.3 1.0 CD C:GLU155 4.9 77.1 1.0 CZ2 C:TRP354 5.0 54.7 1.0

E.M.Jeong, K.B.Lee, G.E.Kim, C.M.Kim, J.H.Lee, H.J.Kim, J.W.Shin, M.A.Kwon, H.H.Park, I.G.Kim. Competitive Binding of Magnesium to Calcium Binding Sites Reciprocally Regulates Transamidase and Gtp Hydrolysis Activity of Transglutaminase 2. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 31991788
DOI: 10.3390/IJMS21030791