Honzatko R B, Hendrickson W A, Love W E
J Mol Biol. 1985 Jul 5;184(1):147-64. doi: 10.1016/0022-2836(85)90049-x.
A molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lamprey Petromyzon marinus yields an R-factor of 0.142 against X-ray diffraction data to 2.0 A resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 A and 1.5 degrees. Atoms that belong to planar groups deviate by 0.012 A from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 A3, 2.0 degrees and 19.4 degrees, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 A2; the variation in thermal parameters for side-chain atoms is 2.13 A2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit. The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 degrees from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 degrees and 1 degree, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-C of the heme (distance = 3.29 A) and CE1 from the pyrrole nitrogen of ring-A (distance = 3.06 A) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.
针对海七鳃鳗（Petromyzon marinus）高铁血红蛋白V与氰化物复合物的蛋白质及周围溶剂构建的分子模型，根据2.0埃分辨率的X射线衍射数据得出的R因子为0.142。与理想键长和键角的均方根偏差分别为0.014埃和1.5度。属于平面基团的原子与通过最小二乘法确定的平面的偏差为0.012埃。手性体积、肽扭转角和侧链扭转角的平均标准偏差分别为0.150埃³、2.0度和19.4度。多肽主链键合原子热参数的均方根变化为1.21埃²；侧链原子热参数的变化为2.13埃²。该模型包含了该蛋白质149个氨基酸残基中11个侧链的多种构象。我们确定了231个位置为水分子的全部或部分占据位点。这些位点的占据因子总和约为154，占晶体学不对称单元内550个水分子的28%。七鳃鳗高铁血红蛋白氰化物复合物中血红素的环境类似于哺乳动物四聚体的脱氧状态。特别是，近端组氨酸的NE2原子与铁之间的键与血红素平面法线的夹角为5.1度。在脱氧血红蛋白和碳氧血红蛋白中，与血红素平面法线的偏差分别为7至8度和1度。此外，近端组氨酸的CD2原子与血红素C环吡咯氮的距离（距离 = 3.29埃）和CE1与A环吡咯氮的距离（距离 = 3.06埃）不相等，这是脱氧血红蛋白的特征，而非碳氧血红蛋白，在碳氧血红蛋白中这些距离是相等的。最后，羰基111与酪氨酸149的羟基之间存在氢键。哺乳动物四聚体中的相应氢键对于T态向R态的转变至关重要，存在于脱氧血红蛋白中但不存在于碳氧血红蛋白中。我们认为，氧气对七鳃鳗血红蛋白的低亲和力可能是这些T态几何结构的结果。
